diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..b197a88 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,27 @@ +# Basic ODK workflow +name: Docs + +# Controls when the action will run. +on: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + push: + branches: + - master + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + build: + name: Deploy docs + runs-on: ubuntu-latest + steps: + - name: Checkout main + uses: actions/checkout@v4 + + - name: Deploy docs + uses: mhausenblas/mkdocs-deploy-gh-pages@master + # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + CONFIG_FILE: mkdocs.yaml + diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml new file mode 100644 index 0000000..f3aae72 --- /dev/null +++ b/.github/workflows/qc.yml @@ -0,0 +1,33 @@ +# Basic ODK workflow + +name: CI + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "ontology_qc" + ontology_qc: + # The type of runner that the job will run on + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.6 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v4 + + - name: Run ontology QC checks + env: + DEFAULT_BRANCH: master + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false + diff --git a/.gitignore b/.gitignore index 9e7bb87..9016a7d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,45 +1,69 @@ -# Compiled class file -*.class - -# Log file -*.log - -# BlueJ files -*.ctxt - -# Mobile Tools for Java (J2ME) -.mtj.tmp/ +# ODK-managed rules, do not modify +# If you need to add your own ignore rules, you may do so below +# the "End ODK-managed rules" marker at the end of this file. +.DS_Store +semantic.cache +bin/ -# Package Files # -*.jar -*.war -*.ear -*.zip -*.tar.gz -*.rar +*.tmp +*.tmp.obo +*.tmp.owl +*.tmp.json +*-relation-graph.tsv.gz +.template.db -# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml -hs_err_pid* +.github/token.txt -.gradle -/build/ +/msio.owl +/msio.obo +/msio.json +/msio.db +/msio-base.* +/msio-basic.* +/msio-full.* +/msio-simple.* +/msio-simple-non-classified.* +/mappings/ +/patterns/ +/reports/ +/subsets/ -# Ignore Gradle GUI config -gradle-app.setting +src/ontology/mirror +src/ontology/mirror/* +src/ontology/reports/* +!src/ontology/reports/release-diff.md +src/ontology/msio.owl +src/ontology/msio.obo +src/ontology/msio.json +src/ontology/msio.db +src/ontology/msio-base.* +src/ontology/msio-basic.* +src/ontology/msio-full.* +src/ontology/msio-simple.* +src/ontology/msio-simple-non-classified.* -# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored) -!gradle-wrapper.jar +src/ontology/seed.txt +src/ontology/dosdp-tools.log +src/ontology/ed_definitions_merged.owl +src/ontology/ontologyterms.txt +src/ontology/simple_seed.txt +src/ontology/patterns +src/ontology/merged-msio-edit.owl +src/ontology/msio-edit.properties -# Cache of project -.gradletasknamecache +src/ontology/target/ +src/ontology/tmp/* +!src/ontology/tmp/.gitkeep +!src/ontology/tmp/README.md -# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898 -# gradle/wrapper/gradle-wrapper.properties +src/ontology/run.sh.conf +src/ontology/run.sh.env -#miscellaneous -.DS_Store -catalog-v001.xml +src/ontology/imports/*_terms_combined.txt +src/patterns/data/**/*.ofn +src/patterns/data/**/*.txt +src/patterns/pattern_owl_seed.txt +src/patterns/all_pattern_terms.txt -# IntelliJ and Gradle -.idea/* +# End of ODK-managed rules diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..fc51143 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,86 @@ +# Contributing to Metabolomics Standards Initiative Ontology + +:+1: First of all: Thank you for taking the time to contribute! + +The following is a set of guidelines for contributing to MSIO. +These guidelines are not strict rules. Use your best judgment, and feel free to propose +changes to this document in a pull request. + +## Table Of Contents + +- [Guidelines for Contributions and Requests](#contributions) + * [Reporting problems with the ontology](#reporting-bugs) + * [Requesting new terms](#requesting-terms) + * [Adding new terms by yourself](#adding-terms) +- [Best practices](#best-practices) + * [How to write a great issue?](#great-issues) + * [How to create a great pull/merge request?](#great-pulls) + + + +## Guidelines for Contributions and Requests + + + +### Reporting problems with the ontology + +Please use our [Issue Tracker](https://github.com/ISA-tools/MSIO - base - full/issues/) for reporting problems with the ontology. +To learn how to write a good issue [see here](#great-issues). + + + +### Requesting new terms + +Before you write a new request, please consider the following: + +- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, +either as a primary term or a synonym term. You can search for your term using [OLS](http://www.ebi.ac.uk/ols/ontologies/msio). +- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be +able to provide a concise definition, ideally with a scientific reference. +- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in +and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope." +It can be very helpful to mention a very similar concept as part of the term request! + +#### Who can request a term? + +Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a +community resource, it is often necessary to do at least some of the work of adding the term yourself, see below. + +#### How to write a new term request + +Request a new term _via_ the GitHub [Issue Tracker](https://github.com/ISA-tools/MSIO - base - full/issues/). + +It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker. +To make this work easier, please always use issue templates if they are available (https://github.com/ISA-tools/MSIO - base - full/issues/new/choose). + +For how to write a good term request, please read the [best practices carefully](#great-issues). + + + +### How to add a new term + +If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies) + +**Process**: + +1. Clone the repository (In case you are not an offical team member, create a fork first) +1. Create new branch in git, for example `git checkout -b issue123` +1. Open src/ontology/msio-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_! +1. Perform your edit and save your changes +1. Commit changes to branch +1. Push changes upstream +1. Create pull request + +## Best Practices + + + +### How to write great issues? + +Please refer to the [OBO Academy term request guide](https://oboacademy.github.io/obook/howto/term-request/). + + + +### How to create a great pull/merge request? + +Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/) \ No newline at end of file diff --git a/Legacy/.gitignore b/Legacy/.gitignore new file mode 100644 index 0000000..9e7bb87 --- /dev/null +++ b/Legacy/.gitignore @@ -0,0 +1,45 @@ +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* + +.gradle +/build/ + +# Ignore Gradle GUI config +gradle-app.setting + +# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored) +!gradle-wrapper.jar + +# Cache of project +.gradletasknamecache + +# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898 +# gradle/wrapper/gradle-wrapper.properties + +#miscellaneous +.DS_Store +catalog-v001.xml + + +# IntelliJ and Gradle +.idea/* diff --git a/CITATION.cff b/Legacy/CITATION.cff similarity index 100% rename from CITATION.cff rename to Legacy/CITATION.cff diff --git a/MSIO-edit.owl b/Legacy/MSIO-edit.owl similarity index 99% rename from MSIO-edit.owl rename to Legacy/MSIO-edit.owl index b501d7c..14e51aa 100644 --- a/MSIO-edit.owl +++ b/Legacy/MSIO-edit.owl @@ -17,13 +17,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - - - - - + Alejandra Gonzalez-Beltran Andrew Lane Hunter Moseley @@ -34,7 +28,6 @@ Vitaly Selivanov Philippe Rocca-Serra an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. - OWL http://creativecommons.org/licenses/by/3.0/ Metabolomics Standards Initiative Ontology (MSIO) https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues @@ -1566,7 +1559,7 @@ last accessed: 2018-01-11 - + diff --git a/Legacy/README.md b/Legacy/README.md new file mode 100644 index 0000000..27f439e --- /dev/null +++ b/Legacy/README.md @@ -0,0 +1,40 @@ +# Metabolomics Standards Initiative Ontology (MSIO) + +MSIO aims to provide a single point of entry to support semantic markup of experiments making use of NMR and MS techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or undertargeted, tracer based applications. MSIO reuses a number of resources such as [CHEBI](https://www.ebi.ac.uk/ols/ontologies/chebi), [DUO](https://www.ebi.ac.uk/ols/ontologies/duo), [NMRCV](https://www.ebi.ac.uk/ols/ontologies/nmrcv), [OBI](https://www.ebi.ac.uk/ols/ontologies/obi), and [STATO](https://www.ebi.ac.uk/ols/ontologies/stato). + +It is compatible with OBI and can be imported in it but also can be used as is for users working solely on Metabolomics. + +MSIO is now available from EMBL EBI Ontology Lookup System, [here.](https://www.ebi.ac.uk/ols/ontologies/msio) + +Log term requests [here.](https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues) + +The following screenshots allow for a sneak peak at the resource to gauge its coverage. +_________ +Material Processing: + +![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-processing.png "Logo Title Text 1") + +_________ +Data Transformation: + +![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-data-transformation.png "Logo Title Text 2") + +_________ +Material Entities: + +![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities.png "Logo Title Text 3") + +_________ +Material Entities: + +![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities-chebi-imports.png "Logo Title Text 4") + +_________ +Information Entities: + +![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-information-entities.png "Logo Title Text 5") + +## Versions + +The development version of the ontology is at: [MSIO-edit.owl](https://raw.githubusercontent.com/ISA-tools/MSIO/master/MSIO-edit.owl) + diff --git a/build.gradle b/Legacy/build.gradle similarity index 100% rename from build.gradle rename to Legacy/build.gradle diff --git a/docs/img/2d_artistic2.gif b/Legacy/docs/img/2d_artistic2.gif similarity index 100% rename from docs/img/2d_artistic2.gif rename to Legacy/docs/img/2d_artistic2.gif diff --git a/docs/img/logo-2121034682.png b/Legacy/docs/img/logo-2121034682.png similarity index 100% rename from docs/img/logo-2121034682.png rename to Legacy/docs/img/logo-2121034682.png diff --git a/docs/img/metsoc-logo.jpeg b/Legacy/docs/img/metsoc-logo.jpeg similarity index 100% rename from docs/img/metsoc-logo.jpeg rename to Legacy/docs/img/metsoc-logo.jpeg diff --git a/docs/img/metsoc2.png b/Legacy/docs/img/metsoc2.png similarity index 100% rename from docs/img/metsoc2.png rename to Legacy/docs/img/metsoc2.png diff --git a/docs/img/msio-data-transformation.png b/Legacy/docs/img/msio-data-transformation.png similarity index 100% rename from docs/img/msio-data-transformation.png rename to Legacy/docs/img/msio-data-transformation.png diff --git a/docs/img/msio-information-entities.png b/Legacy/docs/img/msio-information-entities.png similarity index 100% rename from docs/img/msio-information-entities.png rename to Legacy/docs/img/msio-information-entities.png diff --git a/docs/img/msio-material-entities-chebi-imports.png b/Legacy/docs/img/msio-material-entities-chebi-imports.png similarity index 100% rename from docs/img/msio-material-entities-chebi-imports.png rename to Legacy/docs/img/msio-material-entities-chebi-imports.png diff --git a/docs/img/msio-material-entities.png b/Legacy/docs/img/msio-material-entities.png similarity index 100% rename from docs/img/msio-material-entities.png rename to Legacy/docs/img/msio-material-entities.png diff --git a/docs/img/msio-material-processing.png b/Legacy/docs/img/msio-material-processing.png similarity index 100% rename from docs/img/msio-material-processing.png rename to Legacy/docs/img/msio-material-processing.png diff --git a/duo/MSI_AO_DUO_imports.owl b/Legacy/duo/MSI_AO_DUO_imports.owl similarity index 100% rename from duo/MSI_AO_DUO_imports.owl rename to Legacy/duo/MSI_AO_DUO_imports.owl diff --git a/gradlew b/Legacy/gradlew similarity index 100% rename from gradlew rename to Legacy/gradlew diff --git a/gradlew.bat b/Legacy/gradlew.bat similarity index 100% rename from gradlew.bat rename to Legacy/gradlew.bat diff --git a/nmr/nmrCV.owl b/Legacy/nmr/nmrCV.owl similarity index 100% rename from nmr/nmrCV.owl rename to Legacy/nmr/nmrCV.owl diff --git a/ontofoxInputs/README.md b/Legacy/ontofoxInputs/README.md similarity index 100% rename from ontofoxInputs/README.md rename to Legacy/ontofoxInputs/README.md diff --git a/ontofoxInputs/chebi-lower-terms.txt b/Legacy/ontofoxInputs/chebi-lower-terms.txt similarity index 100% rename from ontofoxInputs/chebi-lower-terms.txt rename to Legacy/ontofoxInputs/chebi-lower-terms.txt diff --git a/ontofoxInputs/chebi-upper-terms.txt b/Legacy/ontofoxInputs/chebi-upper-terms.txt similarity index 100% rename from ontofoxInputs/chebi-upper-terms.txt rename to Legacy/ontofoxInputs/chebi-upper-terms.txt diff --git a/ontofoxInputs/obi-lower-terms.txt b/Legacy/ontofoxInputs/obi-lower-terms.txt similarity index 100% rename from ontofoxInputs/obi-lower-terms.txt rename to Legacy/ontofoxInputs/obi-lower-terms.txt diff --git a/ontofoxInputs/obi-upper-terms.txt b/Legacy/ontofoxInputs/obi-upper-terms.txt similarity index 100% rename from ontofoxInputs/obi-upper-terms.txt rename to Legacy/ontofoxInputs/obi-upper-terms.txt diff --git a/ontofoxInputs/ontofoxInput-OBI-processes.txt b/Legacy/ontofoxInputs/ontofoxInput-OBI-processes.txt similarity index 100% rename from ontofoxInputs/ontofoxInput-OBI-processes.txt rename to Legacy/ontofoxInputs/ontofoxInput-OBI-processes.txt diff --git a/ontofoxInputs/ontofoxInputCHMO.txt b/Legacy/ontofoxInputs/ontofoxInputCHMO.txt similarity index 100% rename from ontofoxInputs/ontofoxInputCHMO.txt rename to Legacy/ontofoxInputs/ontofoxInputCHMO.txt diff --git a/ontofoxInputs/ontofoxInputChEBI-noIntermediates.txt b/Legacy/ontofoxInputs/ontofoxInputChEBI-noIntermediates.txt similarity index 100% rename from ontofoxInputs/ontofoxInputChEBI-noIntermediates.txt rename to Legacy/ontofoxInputs/ontofoxInputChEBI-noIntermediates.txt diff --git a/ontofoxInputs/ontofoxInputChEBI.txt b/Legacy/ontofoxInputs/ontofoxInputChEBI.txt similarity index 100% rename from ontofoxInputs/ontofoxInputChEBI.txt rename to Legacy/ontofoxInputs/ontofoxInputChEBI.txt diff --git a/ontofoxInputs/ontofoxInputIAO.txt b/Legacy/ontofoxInputs/ontofoxInputIAO.txt similarity index 100% rename from ontofoxInputs/ontofoxInputIAO.txt rename to Legacy/ontofoxInputs/ontofoxInputIAO.txt diff --git a/ontofoxInputs/ontofoxInputPSI-MS.txt b/Legacy/ontofoxInputs/ontofoxInputPSI-MS.txt similarity index 100% rename from ontofoxInputs/ontofoxInputPSI-MS.txt rename to Legacy/ontofoxInputs/ontofoxInputPSI-MS.txt diff --git a/ontofoxInputs/ontofoxInputUO.txt b/Legacy/ontofoxInputs/ontofoxInputUO.txt similarity index 100% rename from ontofoxInputs/ontofoxInputUO.txt rename to Legacy/ontofoxInputs/ontofoxInputUO.txt diff --git a/ontofoxOutputs/MSIO-CHMO_import.owl b/Legacy/ontofoxOutputs/MSIO-CHMO_import.owl similarity index 100% rename from ontofoxOutputs/MSIO-CHMO_import.owl rename to Legacy/ontofoxOutputs/MSIO-CHMO_import.owl diff --git a/ontofoxOutputs/MSIO_ChEBI_import.owl b/Legacy/ontofoxOutputs/MSIO_ChEBI_import.owl similarity index 100% rename from ontofoxOutputs/MSIO_ChEBI_import.owl rename to Legacy/ontofoxOutputs/MSIO_ChEBI_import.owl diff --git a/ontofoxOutputs/MSIO_OBI_import.owl b/Legacy/ontofoxOutputs/MSIO_OBI_import.owl similarity index 100% rename from ontofoxOutputs/MSIO_OBI_import.owl rename to Legacy/ontofoxOutputs/MSIO_OBI_import.owl diff --git a/ontofoxOutputs/MSIO_PSIMS_import.owl b/Legacy/ontofoxOutputs/MSIO_PSIMS_import.owl similarity index 100% rename from ontofoxOutputs/MSIO_PSIMS_import.owl rename to Legacy/ontofoxOutputs/MSIO_PSIMS_import.owl diff --git a/ontofoxOutputs/MSIO_UO_import.owl b/Legacy/ontofoxOutputs/MSIO_UO_import.owl similarity index 100% rename from ontofoxOutputs/MSIO_UO_import.owl rename to Legacy/ontofoxOutputs/MSIO_UO_import.owl diff --git a/releases/1.0.1/MSIO-merged-reasoned.obo b/Legacy/releases/1.0.1/MSIO-merged-reasoned.obo similarity index 100% rename from releases/1.0.1/MSIO-merged-reasoned.obo rename to Legacy/releases/1.0.1/MSIO-merged-reasoned.obo diff --git a/releases/1.0.1/MSIO-merged-reasoned.owl b/Legacy/releases/1.0.1/MSIO-merged-reasoned.owl similarity index 100% rename from releases/1.0.1/MSIO-merged-reasoned.owl rename to Legacy/releases/1.0.1/MSIO-merged-reasoned.owl diff --git a/releases/1.0/MSIO-merged-reasoned.obo b/Legacy/releases/1.0/MSIO-merged-reasoned.obo similarity index 100% rename from releases/1.0/MSIO-merged-reasoned.obo rename to Legacy/releases/1.0/MSIO-merged-reasoned.obo diff --git a/releases/1.0/MSIO-merged-reasoned.owl b/Legacy/releases/1.0/MSIO-merged-reasoned.owl similarity index 100% rename from releases/1.0/MSIO-merged-reasoned.owl rename to Legacy/releases/1.0/MSIO-merged-reasoned.owl diff --git a/releases/latest_release/MSIO-merged-reasoned.obo b/Legacy/releases/latest_release/MSIO-merged-reasoned.obo similarity index 100% rename from releases/latest_release/MSIO-merged-reasoned.obo rename to Legacy/releases/latest_release/MSIO-merged-reasoned.obo diff --git a/releases/latest_release/MSIO-merged-reasoned.owl b/Legacy/releases/latest_release/MSIO-merged-reasoned.owl similarity index 100% rename from releases/latest_release/MSIO-merged-reasoned.owl rename to Legacy/releases/latest_release/MSIO-merged-reasoned.owl diff --git a/settings.gradle b/Legacy/settings.gradle similarity index 100% rename from settings.gradle rename to Legacy/settings.gradle diff --git a/src/main/java/OntoFoxInput.java b/Legacy/src/main/java/OntoFoxInput.java similarity index 100% rename from src/main/java/OntoFoxInput.java rename to Legacy/src/main/java/OntoFoxInput.java diff --git a/src/main/java/OntoFoxInputParser.java b/Legacy/src/main/java/OntoFoxInputParser.java similarity index 100% rename from src/main/java/OntoFoxInputParser.java rename to Legacy/src/main/java/OntoFoxInputParser.java diff --git a/Legacy/src/ontology/Makefile b/Legacy/src/ontology/Makefile new file mode 100644 index 0000000..fb0a35c --- /dev/null +++ b/Legacy/src/ontology/Makefile @@ -0,0 +1,30 @@ +OBO=http://purl.obolibrary.org/obo +ONT=MSIO +BASE=$(OBO)/$(ONT) +SRC=../../$(ONT)-edit.owl +RELEASEDIR=./releases +IMPORTSDIR=./imports +ROBOT-PLUS=../../bin/robot-plus +GRADLE=gradle + +all: $(ONT).owl + +test:all + +$(ONT).owl: $(SRC) + $(ROBOT-PLUS) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ + +prepare_release: + $(GRADLE) clean + $(GRADLE) jar + cp ./build/libs/robot-plus.jar ./bin/ + export PATH=$(PATH):$(PWD)/bin + + $(ROBOT-PLUS) merge -I "http://purl.obolibrary.org/obo/duo.owl" extract --method MIREOT \ + --upper-term "owl:Thing" --lower-term "obo:DUO_0000001" --lower-term "obo:DUO_0000017" \ + --branch-from-term "obo:DUO_0000001" --branch-from-term "obo:DUO_0000017" \ + --output $(IMPORTSDIR)/duo_import.owl + + +duo_import: + cd ./imports/duo/; pwd; ../../$(ROBOT-PLUS) query -I "http://purl.obolibrary.org/obo/duo.owl" -query descendants.sparql duo-terms-file.txt; ../../$(ROBOT-PLUS) extract --method BOT -I "http://purl.obolibrary.org/obo/duo.owl" --term-file duo-terms-file.txt --output ../MSIO_DUO_import.owl diff --git a/src/ontology/imports/MSIO_DUO_import.owl b/Legacy/src/ontology/imports/MSIO_DUO_import.owl similarity index 100% rename from src/ontology/imports/MSIO_DUO_import.owl rename to Legacy/src/ontology/imports/MSIO_DUO_import.owl diff --git a/src/ontology/imports/duo/.gitignore b/Legacy/src/ontology/imports/duo/.gitignore similarity index 100% rename from src/ontology/imports/duo/.gitignore rename to Legacy/src/ontology/imports/duo/.gitignore diff --git a/src/ontology/imports/duo/README.md b/Legacy/src/ontology/imports/duo/README.md similarity index 100% rename from src/ontology/imports/duo/README.md rename to Legacy/src/ontology/imports/duo/README.md diff --git a/src/ontology/imports/duo/descendants.sparql b/Legacy/src/ontology/imports/duo/descendants.sparql similarity index 100% rename from src/ontology/imports/duo/descendants.sparql rename to Legacy/src/ontology/imports/duo/descendants.sparql diff --git a/src/test/java/OntoFoxInputParserTest.java b/Legacy/src/test/java/OntoFoxInputParserTest.java similarity index 100% rename from src/test/java/OntoFoxInputParserTest.java rename to Legacy/src/test/java/OntoFoxInputParserTest.java diff --git a/src/test/resources/input1.txt b/Legacy/src/test/resources/input1.txt similarity index 100% rename from src/test/resources/input1.txt rename to Legacy/src/test/resources/input1.txt diff --git a/src/test/resources/ontofoxInput-OBI-processes.txt b/Legacy/src/test/resources/ontofoxInput-OBI-processes.txt similarity index 100% rename from src/test/resources/ontofoxInput-OBI-processes.txt rename to Legacy/src/test/resources/ontofoxInput-OBI-processes.txt diff --git a/src/test/resources/ontofoxInputUO.txt b/Legacy/src/test/resources/ontofoxInputUO.txt similarity index 100% rename from src/test/resources/ontofoxInputUO.txt rename to Legacy/src/test/resources/ontofoxInputUO.txt diff --git a/stato/stato14pre.owl b/Legacy/stato/stato14pre.owl similarity index 100% rename from stato/stato14pre.owl rename to Legacy/stato/stato14pre.owl diff --git a/gradle/wrapper/gradle-wrapper.jar b/Legacy/wrapper/gradle-wrapper.jar similarity index 100% rename from gradle/wrapper/gradle-wrapper.jar rename to Legacy/wrapper/gradle-wrapper.jar diff --git a/gradle/wrapper/gradle-wrapper.properties b/Legacy/wrapper/gradle-wrapper.properties similarity index 100% rename from gradle/wrapper/gradle-wrapper.properties rename to Legacy/wrapper/gradle-wrapper.properties diff --git a/README.md b/README.md index 27f439e..8a746b8 100644 --- a/README.md +++ b/README.md @@ -1,40 +1,29 @@ -# Metabolomics Standards Initiative Ontology (MSIO) -MSIO aims to provide a single point of entry to support semantic markup of experiments making use of NMR and MS techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or undertargeted, tracer based applications. MSIO reuses a number of resources such as [CHEBI](https://www.ebi.ac.uk/ols/ontologies/chebi), [DUO](https://www.ebi.ac.uk/ols/ontologies/duo), [NMRCV](https://www.ebi.ac.uk/ols/ontologies/nmrcv), [OBI](https://www.ebi.ac.uk/ols/ontologies/obi), and [STATO](https://www.ebi.ac.uk/ols/ontologies/stato). +![Build Status](https://github.com/ISA-tools/MSIO - base - full/actions/workflows/qc.yml/badge.svg) +# Metabolomics Standards Initiative Ontology -It is compatible with OBI and can be imported in it but also can be used as is for users working solely on Metabolomics. +Description: None -MSIO is now available from EMBL EBI Ontology Lookup System, [here.](https://www.ebi.ac.uk/ols/ontologies/msio) +More information can be found at http://obofoundry.org/ontology/msio -Log term requests [here.](https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues) - -The following screenshots allow for a sneak peak at the resource to gauge its coverage. -_________ -Material Processing: - -![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-processing.png "Logo Title Text 1") +## Versions -_________ -Data Transformation: +### Stable release versions -![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-data-transformation.png "Logo Title Text 2") +The latest version of the ontology can always be found at: -_________ -Material Entities: +http://purl.obolibrary.org/obo/msio.owl -![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities.png "Logo Title Text 3") +(note this will not show up until the request has been approved by obofoundry.org) -_________ -Material Entities: +### Editors' version -![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities-chebi-imports.png "Logo Title Text 4") +Editors of this ontology should use the edit version, [src/ontology/msio-edit.owl](src/ontology/msio-edit.owl) -_________ -Information Entities: +## Contact -![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-information-entities.png "Logo Title Text 5") +Please use this GitHub repository's [Issue tracker](https://github.com/ISA-tools/MSIO - base - full/issues) to request new terms/classes or report errors or specific concerns related to the ontology. -## Versions +## Acknowledgements -The development version of the ontology is at: [MSIO-edit.owl](https://raw.githubusercontent.com/ISA-tools/MSIO/master/MSIO-edit.owl) - +This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit). \ No newline at end of file diff --git a/bin/robot-plus b/bin/robot-plus deleted file mode 100755 index ff58cb9..0000000 --- a/bin/robot-plus +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env bash - -## Check for Cygwin, use grep for a case-insensitive search -IS_CYGWIN="FALSE" -if uname | grep -iq cygwin; then - IS_CYGWIN="TRUE" -fi - -DIR="$( cd "$( dirname "$0" )" && pwd )" - -if [ $IS_CYGWIN = "TRUE" ] -then - exec java $ROBOT_JAVA_ARGS -jar "$(cygpath -w $DIR/../build/libs/robot-plus.jar)" "$@" -else - exec java $ROBOT_JAVA_ARGS -jar "$DIR/../build/libs/robot-plus.jar" "$@" -fi diff --git a/bin/robot-plus.bat b/bin/robot-plus.bat deleted file mode 100755 index 70035dd..0000000 --- a/bin/robot-plus.bat +++ /dev/null @@ -1 +0,0 @@ -java -jar %~dp0robot.jar %* \ No newline at end of file diff --git a/issue_template.md b/issue_template.md new file mode 100644 index 0000000..061074e --- /dev/null +++ b/issue_template.md @@ -0,0 +1,21 @@ +For new term requests, please provide the following information: + +## Preferred term label + +(e.g., Asplenia) + +## Synonyms + +(e.g., Absent spleen) + +## Textual definition + +the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term. + +## Suggested parent term + +Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/msio) + +## Attribution + +If you would like a nanoattribution, please indicate your ORCID id \ No newline at end of file diff --git a/libs/robot.jar b/libs/robot.jar deleted file mode 100644 index 3c43d21..0000000 Binary files a/libs/robot.jar and /dev/null differ diff --git a/msio-odk.yaml b/msio-odk.yaml new file mode 100755 index 0000000..b30efb2 --- /dev/null +++ b/msio-odk.yaml @@ -0,0 +1,65 @@ +id: msio +title: "Metabolomics Standards Initiative Ontology" +github_org: ISA-tools +git_main_branch: master +repo: MSIO + - base + - full +primary_release: full +export_formats: + - owl + - obo + - json +import_group: + use_base_merging: TRUE + products: + - id: iao + - id: cl + use_base: TRUE + - id: obi + use_base: TRUE + - id: chebi + mirror_from: https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/refs/heads/main/chebi_slim.owl + is_large: TRUE + - id: duo + make_base: TRUE + - id: ro + use_base: TRUE + - id: nmrCV + mirror_from: http://nmrml.org/cv/v1.1.0/nmrCV.owl + make_base: TRUE + base_iris: + - http://nmrML.org/nmrCV# + - id: chmo + use_base: TRUE + - id: gaz + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/gaz_ + - id: go + use_base: TRUE + - id: ms + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/MS_ + - id: ncbitaxon + mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl + - id: pato + use_base: TRUE + - id: uo + make_base: TRUE + - id: ogms + make_base: TRUE + - id: pr + make_base: TRUE + mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl + is_large: TRUE + - id: so + make_base: TRUE +robot_java_args: "-Xmx16G" +robot_report: + use_labels: TRUE + fail_on: ERROR + custom_profile: TRUE + report_on: + - edit \ No newline at end of file diff --git a/seed-via-docker.sh b/seed-via-docker.sh new file mode 100644 index 0000000..15d163c --- /dev/null +++ b/seed-via-docker.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +echo "This script only works with ODK 1.3.2 and later. For ODK 1.3.1 or earlier, use https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh" + +ODK_IMAGE=${ODK_IMAGE:-odkfull} +ODK_TAG=${ODK_TAG:-latest} +ODK_GITNAME=${ODK_GITNAME:-$(git config --get user.name)} +ODK_GITEMAIL=${ODK_GITEMAIL:-$(git config --get user.email)} + +docker run -e ODK_USER_ID=$(id -u) -e ODK_GROUP_ID=$(id -g) -v $PWD:/work -w /work --rm obolibrary/$ODK_IMAGE:$ODK_TAG /tools/odk.py seed --gitname "$ODK_GITNAME" --gitemail "$ODK_GITEMAIL" "$@" \ No newline at end of file diff --git a/src/metadata/README.md b/src/metadata/README.md new file mode 100644 index 0000000..9b3ba61 --- /dev/null +++ b/src/metadata/README.md @@ -0,0 +1,24 @@ +Metadata files for the OBO Library + + * [msio.yml](msio.yml) + * Determines how your purl.obolibrary.org/obo/msio/ redirects will be handled + * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config + * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config) + * Paste in the contents of [msio.yml](msio.yml) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + * [msio.md](msio.md) + * Determines how your metadata is shown on OBO Library, OLS and AberOWL + * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology + * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology) + * Paste in the contents of [msio.md](msio.md) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + +For more background see: + + * http://obofoundry.org/ + * http://obofoundry.org/faq/how-do-i-edit-metadata.html + diff --git a/src/metadata/msio.md b/src/metadata/msio.md new file mode 100644 index 0000000..845fe7c --- /dev/null +++ b/src/metadata/msio.md @@ -0,0 +1,59 @@ +--- +layout: ontology_detail +id: msio +title: Metabolomics Standards Initiative Ontology +jobs: + - id: https://travis-ci.org/ISA-tools/MSIO - base - full + type: travis-ci +build: + checkout: git clone https://github.com/ISA-tools/MSIO - base - full.git + system: git + path: "." +contact: + email: + label: + github: +description: Metabolomics Standards Initiative Ontology is an ontology... +domain: stuff +homepage: https://github.com/ISA-tools/MSIO - base - full +products: + - id: msio.owl + name: "Metabolomics Standards Initiative Ontology main release in OWL format" + - id: msio.obo + name: "Metabolomics Standards Initiative Ontology additional release in OBO format" + - id: msio.json + name: "Metabolomics Standards Initiative Ontology additional release in OBOJSon format" + - id: msio/msio-base.owl + name: "Metabolomics Standards Initiative Ontology main release in OWL format" + - id: msio/msio-base.obo + name: "Metabolomics Standards Initiative Ontology additional release in OBO format" + - id: msio/msio-base.json + name: "Metabolomics Standards Initiative Ontology additional release in OBOJSon format" +dependencies: +- id: iao +- id: cl +- id: obi +- id: chebi +- id: duo +- id: ro +- id: nmrCV +- id: chmo +- id: gaz +- id: go +- id: ms +- id: ncbitaxon +- id: pato +- id: uo +- id: ogms +- id: pr +- id: so +tracker: https://github.com/ISA-tools/MSIO - base - full/issues +license: + url: http://creativecommons.org/licenses/by/3.0/ + label: CC-BY +activity_status: active +--- + +Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML. +You can also embed images too. + diff --git a/src/metadata/msio.yml b/src/metadata/msio.yml new file mode 100644 index 0000000..e665db6 --- /dev/null +++ b/src/metadata/msio.yml @@ -0,0 +1,28 @@ +# PURL configuration for http://purl.obolibrary.org/obo/msio + +idspace: MSIO +base_url: /obo/msio + +products: +- msio.owl: https://raw.githubusercontent.com/ISA-tools/MSIO - base - full/master/msio.owl +- msio.obo: https://raw.githubusercontent.com/ISA-tools/MSIO - base - full/master/msio.obo + +term_browser: ontobee +example_terms: +- MSIO_0000000 + +entries: + +- prefix: /releases/ + replacement: https://raw.githubusercontent.com/ISA-tools/MSIO - base - full/v + +- prefix: /tracker/ + replacement: https://github.com/ISA-tools/MSIO - base - full/issues + +- prefix: /about/ + replacement: http://www.ontobee.org/ontology/MSIO?iri=http://purl.obolibrary.org/obo/ + +## generic fall-through, serve direct from github by default +- prefix: / + replacement: https://raw.githubusercontent.com/ISA-tools/MSIO - base - full/master/ + diff --git a/src/ontology/Makefile b/src/ontology/Makefile index fb0a35c..1b8f070 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,30 +1,836 @@ -OBO=http://purl.obolibrary.org/obo -ONT=MSIO -BASE=$(OBO)/$(ONT) -SRC=../../$(ONT)-edit.owl -RELEASEDIR=./releases -IMPORTSDIR=./imports -ROBOT-PLUS=../../bin/robot-plus -GRADLE=gradle +# ---------------------------------------- +# Makefile for msio +# Generated using ontology-development-kit +# ODK Version: v1.6 +# ---------------------------------------- +# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use msio.Makefile instead -all: $(ONT).owl -test:all +# ---------------------------------------- +# More information: https://github.com/INCATools/ontology-development-kit/ -$(ONT).owl: $(SRC) - $(ROBOT-PLUS) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= fc938b7a2a799bf84363224dad3f17b5a8a2d2866c92dd4613b6169e1c323aa0 -prepare_release: - $(GRADLE) clean - $(GRADLE) jar - cp ./build/libs/robot-plus.jar ./bin/ - export PATH=$(PATH):$(PWD)/bin - $(ROBOT-PLUS) merge -I "http://purl.obolibrary.org/obo/duo.owl" extract --method MIREOT \ - --upper-term "owl:Thing" --lower-term "obo:DUO_0000001" --lower-term "obo:DUO_0000017" \ - --branch-from-term "obo:DUO_0000001" --branch-from-term "obo:DUO_0000017" \ - --output $(IMPORTSDIR)/duo_import.owl +# ---------------------------------------- +# Standard Constants +# ---------------------------------------- +# these can be overwritten on the command line +OBOBASE= http://purl.obolibrary.org/obo +URIBASE= http://purl.obolibrary.org/obo +ONT= msio +ONTBASE= http://purl.obolibrary.org/obo/msio +EDIT_FORMAT= owl +SRC = $(ONT)-edit.$(EDIT_FORMAT) +MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false +CATALOG= catalog-v001.xml +ROBOT= robot --catalog $(CATALOG) +REASONER= ELK +OWLTOOLS = owltools --use-catalog +RELEASEDIR= ../.. +DOCSDIR= ../../docs +REPORTDIR= reports +TEMPLATEDIR= ../templates +TMPDIR= tmp +MIRRORDIR= mirror +IMPORTDIR= imports +SUBSETDIR= subsets +SCRIPTSDIR= ../scripts +UPDATEREPODIR= target +SPARQLDIR = ../sparql +EXTENDED_PREFIX_MAP= $(TMPDIR)/obo.epm.json +COMPONENTSDIR = components +ROBOT_PROFILE = profile.txt +REPORT_FAIL_ON = ERROR +REPORT_LABEL = -l true +REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) +OBO_FORMAT_OPTIONS = --clean-obo "strict drop-untranslatable-axioms" +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.6 +RELAX_OPTIONS = --include-subclass-of true +REDUCE_OPTIONS = --include-subproperties true -duo_import: - cd ./imports/duo/; pwd; ../../$(ROBOT-PLUS) query -I "http://purl.obolibrary.org/obo/duo.owl" -query descendants.sparql duo-terms-file.txt; ../../$(ROBOT-PLUS) extract --method BOT -I "http://purl.obolibrary.org/obo/duo.owl" --term-file duo-terms-file.txt --output ../MSIO_DUO_import.owl +TODAY ?= $(shell date +%Y-%m-%d) +OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') +VERSION= $(TODAY) +ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) +ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ +OTHER_SRC = +ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt +EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl + + +FORMATS = $(sort owl obo json owl) +FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) +RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base ) + +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif + +# ---------------------------------------- +# Workflow control +# ---------------------------------------- +# Set any of the following variables to false to completely disable the +# corresponding workflows. + +# Refresh of mirrors (and all remote resources more generally) +MIR = true + +# Re-generation of import modules +IMP = true + +# Re-generation of "large" import modules +# Note that IMP=false takes precedence over IMP_LARGE=true, that is, +# IMP=false disables the generation of all import modules, large or not. +IMP_LARGE = true + +# Re-generation of component modules +COMP = true + +# Re-generation of pattern-derived files +PAT = true + +# ---------------------------------------- +# Top-level targets +# ---------------------------------------- + +.PHONY: .FORCE + +.PHONY: all +all: all_odk + +.PHONY: all_odk +all_odk: odkversion config_check test custom_reports all_assets + +.PHONY: test +test: odkversion validate_idranges reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt + echo "Finished running all tests successfully." + +.PHONY: test +test_fast: + $(MAKE_FAST) test + +.PHONY: release_diff +release_diff: $(REPORTDIR)/release-diff.md + +.PHONY: reason_test +reason_test: $(EDIT_PREPROCESSED) + $(ROBOT) reason --input $< --reasoner $(REASONER) --equivalent-classes-allowed asserted-only \ + --exclude-tautologies structural --output test.owl && rm test.owl + +.PHONY: odkversion +odkversion: + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(tr -d '\r' < $(ONT)-odk.yaml | sha256sum | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + + +$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): + mkdir -p $@ + +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in msio.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + +# ---------------------------------------- +# Release assets +# ---------------------------------------- + +MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT)) +MAIN_GZIPPED = +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +SRCMERGED = $(TMPDIR)/merged-$(ONT)-edit.ofn + +.PHONY: all_main +all_main: $(MAIN_FILES) + +# ---------------------------------------- +# Import assets +# ---------------------------------------- + + +IMPORTS = iao cl obi chebi duo ro nmrCV chmo go ms ncbitaxon pato uo ogms pr so + +IMPORT_ROOTS = $(IMPORTDIR)/merged_import +IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) +IMPORT_FILES = $(IMPORT_OWL_FILES) + + +.PHONY: all_imports +all_imports: $(IMPORT_FILES) + +# ---------------------------------------- +# Subset assets +# ---------------------------------------- + + +SUBSETS = + +SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) +SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) + +.PHONY: all_subsets +all_subsets: $(SUBSET_FILES) + +# ---------------------------------------- +# Mapping assets +# ---------------------------------------- + + +MAPPINGS = + + +MAPPING_FILES = $(foreach p, $(MAPPINGS), $(MAPPINGDIR)/$(p).sssom.tsv) +RELEASED_MAPPING_FILES = $(foreach p, $(RELEASED_MAPPINGS), $(MAPPINGDIR)/$(p).sssom.tsv) + +.PHONY: all_mappings +all_mappings: $(MAPPING_FILES) + + +# ---------------------------------------- +# QC Reports & Utilities +# ---------------------------------------- + +OBO_REPORT = $(SRC)-obo-report +ALIGNMENT_REPORT = $(SRC)-align-report +REPORTS = $(OBO_REPORT) +REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) + +.PHONY: robot_reports +robot_reports: $(REPORT_FILES) + +.PHONY: all_reports +all_reports: custom_reports robot_reports + +# ---------------------------------------- +# ROBOT OWL Profile checking +# ---------------------------------------- + +# The merge step is necessary to avoid undeclared entity violations. +$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR) + $(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn + $(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; } +.PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt + +validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt + echo "$* profile validation completed." + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- + +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live. + +SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) + +sparql_test: $(SRCMERGED) | $(REPORTDIR) +ifneq ($(SPARQL_VALIDATION_QUERIES),) + + $(ROBOT) verify -i $(SRCMERGED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) +endif + +# ---------------------------------------- +# ROBOT report +# ---------------------------------------- + +$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ + +$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ + +check_for_robot_updates: + @cut -f2 "/tools/templates/src/ontology/profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt + @cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt + @comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt + @echo "Missing tests:" + @cat $(TMPDIR)/missing.txt + @rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt + +# ---------------------------------------- +# Release assets +# ---------------------------------------- + +ASSETS = \ + $(IMPORT_FILES) \ + $(MAIN_FILES) \ + $(REPORT_FILES) \ + $(SUBSET_FILES) \ + $(MAPPING_FILES) + +RELEASE_ASSETS = \ + $(MAIN_FILES) \ + $(SUBSET_FILES) + +.PHONY: all_assets +all_assets: $(ASSETS) check_rdfxml_assets + +.PHONY: show_assets +show_assets: + echo $(ASSETS) + du -sh $(ASSETS) + +check_rdfxml_%: % + @check-rdfxml $< + +.PHONY: check_rdfxml_assets +check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) + +# ---------------------------------------- +# Release Management +# ---------------------------------------- + +CLEANFILES=$(MAIN_FILES) $(SRCMERGED) $(EDIT_PREPROCESSED) + +# This should be executed by the release manager whenever time comes to make a release. +# It will ensure that all assets/files are fresh, and will copy to release folder +.PHONY: prepare_release +prepare_release: all_odk + $(MAKE) copy_release_files + rm -f $(CLEANFILES) + @echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \ + on your git hosting site such as GitHub or GitLab" + +.PHONY: prepare_release_fast +prepare_release_fast: + $(MAKE) prepare_release IMP=false PAT=false MIR=false COMP=false + +# This rule does the bulk of the work for prepare_release, copying all +# files to the release directory. It is mostly intended for internal +# use, by the prepare_release rule itself or by other ODK scripts. +.PHONY: copy_release_files +copy_release_files: + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) + +# All released assets, in their final location within the release +RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), $(RELEASEDIR)/$(n)) + +.PHONY: show_release_assets +show_release_assets: + @echo $(RELEASE_ASSETS_AFTER_RELEASE) + +CURRENT_RELEASE=$(ONTBASE).owl + +$(TMPDIR)/current-release.owl: + wget $(CURRENT_RELEASE) -O $@ + +$(REPORTDIR)/release-diff.md: $(ONT).owl $(TMPDIR)/current-release.owl + $(ROBOT) diff --labels true --left $(TMPDIR)/current-release.owl --right $(ONT).owl -f markdown -o $@ + +# ------------------------ +# Imports: Seeding system +# ------------------------ + +# pre_seed.txt contains all entities referenced from the -edit file +# and its components +PRESEED=$(TMPDIR)/pre_seed.txt +$(PRESEED): $(SRCMERGED) + $(ROBOT) query --input $< --format --csv \ + --query $(SPARQLDIR)/terms.sparql $@ + +$(SRCMERGED): $(EDIT_PREPROCESSED) $(OTHER_SRC) + $(ROBOT) remove --input $< --select imports --trim false \ + merge $(foreach src, $(OTHER_SRC), --input $(src)) \ + --output $@ + +$(EDIT_PREPROCESSED): $(SRC) + $(ROBOT) convert --input $< --format ofn --output $@ + +# seed.txt contains all entities to import in addition to those defined +# in the individual _terms.txt files. +IMPORTSEED = $(TMPDIR)/seed.txt +$(IMPORTSEED): $(PRESEED) | $(TMPDIR) + cat $^ | sort | uniq > $@ + +T_IMPORTSEED = --term-file $(IMPORTSEED) + +ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 OMO:0002000 + +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder +# This pattern uses ROBOT to generate an import module + +ifeq ($(IMP),true) + +ALL_TERMS = $(foreach imp, $(IMPORTS), $(IMPORTDIR)/$(imp)_terms.txt) + +$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(ALL_TERMS) \ + $(IMPORTSEED) | all_robot_plugins + $(ROBOT) merge --input $< \ + extract $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \ + --force true --copy-ontology-annotations false \ + --individuals include \ + --method BOT \ + remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \ + $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \ + --select complement --select annotation-properties \ + odk:normalize --base-iri http://purl.obolibrary.org/obo \ + --subset-decls true --synonym-decls true \ + repair --merge-axiom-annotations true \ + $(ANNOTATE_CONVERT_FILE) + +endif # IMP=true + +.PHONY: refresh-imports +refresh-imports: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true clean all_imports + +.PHONY: no-mirror-refresh-imports +no-mirror-refresh-imports: + $(MAKE) --assume-new=$(SRC) \ + $(foreach imp,$(IMPORTS),--assume-new=$(IMPORTDIR)/$(imp)_terms.txt) \ + IMP=true MIR=false PAT=false IMP_LARGE=true all_imports + +.PHONY: refresh-imports-excluding-large +refresh-imports-excluding-large: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false clean all_imports + +.PHONY: refresh-% +refresh-%: + $(MAKE) --assume-new=$(SRC) --assume-new=$(IMPORTDIR)/$*_terms.txt \ + IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl + +.PHONY: no-mirror-refresh-% +no-mirror-refresh-%: + $(MAKE) --assume-new=$(SRC) --assume-new=$(IMPORTDIR)/$*_terms.txt \ + IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl + +# ---------------------------------------- +# Mirroring upstream ontologies +# ---------------------------------------- + +ifeq ($(MIR),true) + + +## ONTOLOGY: iao +.PHONY: mirror-iao +.PRECIOUS: $(MIRRORDIR)/iao.owl +mirror-iao: | $(TMPDIR) + curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: cl +.PHONY: mirror-cl +.PRECIOUS: $(MIRRORDIR)/cl.owl +mirror-cl: | $(TMPDIR) + curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(TMPDIR)/cl-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/cl-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: obi +.PHONY: mirror-obi +.PRECIOUS: $(MIRRORDIR)/obi.owl +mirror-obi: | $(TMPDIR) + curl -L $(OBOBASE)/obi/obi-base.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: chebi +.PHONY: mirror-chebi +.PRECIOUS: $(MIRRORDIR)/chebi.owl +ifeq ($(IMP_LARGE),true) +mirror-chebi: | $(TMPDIR) + $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/refs/heads/main/chebi_slim.owl -o $(TMPDIR)/$@.owl +endif + + +## ONTOLOGY: duo +.PHONY: mirror-duo +.PRECIOUS: $(MIRRORDIR)/duo.owl +mirror-duo: | $(TMPDIR) + curl -L $(OBOBASE)/duo.owl --create-dirs -o $(TMPDIR)/duo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/duo-download.owl --base-iri http://purl.obolibrary.org/obo/DUO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: ro +.PHONY: mirror-ro +.PRECIOUS: $(MIRRORDIR)/ro.owl +mirror-ro: | $(TMPDIR) + curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: nmrCV +.PHONY: mirror-nmrCV +.PRECIOUS: $(MIRRORDIR)/nmrCV.owl +mirror-nmrCV: | $(TMPDIR) + $(ROBOT) remove -I http://nmrml.org/cv/v1.1.0/nmrCV.owl --base-iri http://nmrML.org/nmrCV# --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: chmo +.PHONY: mirror-chmo +.PRECIOUS: $(MIRRORDIR)/chmo.owl +mirror-chmo: | $(TMPDIR) + curl -L $(OBOBASE)/chmo/chmo-base.owl --create-dirs -o $(TMPDIR)/chmo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/chmo-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: go +.PHONY: mirror-go +.PRECIOUS: $(MIRRORDIR)/go.owl +mirror-go: | $(TMPDIR) + curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: ms +.PHONY: mirror-ms +.PRECIOUS: $(MIRRORDIR)/ms.owl +mirror-ms: | $(TMPDIR) + curl -L $(OBOBASE)/ms.owl --create-dirs -o $(TMPDIR)/ms-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/ms-download.owl --base-iri http://purl.obolibrary.org/obo/MS_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: ncbitaxon +.PHONY: mirror-ncbitaxon +.PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl +mirror-ncbitaxon: | $(TMPDIR) + $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: pato +.PHONY: mirror-pato +.PRECIOUS: $(MIRRORDIR)/pato.owl +mirror-pato: | $(TMPDIR) + curl -L $(OBOBASE)/pato/pato-base.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/pato-download.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: uo +.PHONY: mirror-uo +.PRECIOUS: $(MIRRORDIR)/uo.owl +mirror-uo: | $(TMPDIR) + curl -L $(OBOBASE)/uo.owl --create-dirs -o $(TMPDIR)/uo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/uo-download.owl --base-iri http://purl.obolibrary.org/obo/UO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: ogms +.PHONY: mirror-ogms +.PRECIOUS: $(MIRRORDIR)/ogms.owl +mirror-ogms: | $(TMPDIR) + curl -L $(OBOBASE)/ogms.owl --create-dirs -o $(TMPDIR)/ogms-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/ogms-download.owl --base-iri http://purl.obolibrary.org/obo/OGMS --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: pr +.PHONY: mirror-pr +.PRECIOUS: $(MIRRORDIR)/pr.owl +ifeq ($(IMP_LARGE),true) +mirror-pr: | $(TMPDIR) + $(ROBOT) remove -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl --base-iri http://purl.obolibrary.org/obo/PR --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl +endif + + +## ONTOLOGY: so +.PHONY: mirror-so +.PRECIOUS: $(MIRRORDIR)/so.owl +mirror-so: | $(TMPDIR) + curl -L $(OBOBASE)/so.owl --create-dirs -o $(TMPDIR)/so-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/so-download.owl --base-iri http://purl.obolibrary.org/obo/SO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + +ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) +MERGE_MIRRORS = true + +ifeq ($(MERGE_MIRRORS),true) +$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS) + $(ROBOT) merge $(patsubst %, -i %, $^) -o $@ +.PRECIOUS: $(MIRRORDIR)/merged.owl +endif + + +$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) + if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + cp $(TMPDIR)/mirror-$*.owl $@; fi; fi + +endif # MIR=true + + + +# ---------------------------------------- +# Subsets +# ---------------------------------------- +$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl + $(ROBOT) export -i $< --include classes \ + --header "ID [IRI]|LABEL" --format tsv --export $@ +.PRECIOUS: $(SUBSETDIR)/%.tsv + +$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) all_robot_plugins + $(ROBOT) odk:subset -i $< --subset $* --fill-gaps true \ + annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@ +.PRECIOUS: $(SUBSETDIR)/%.owl + + +$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@ + +$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl + $(ROBOT) convert --input $< --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ + + +# --------------------------------------------- +# Sparql queries: Table exports / Query Reports +# --------------------------------------------- + +SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv) +# This combines all into one single command + +.PHONY: custom_reports +custom_reports: $(EDIT_PREPROCESSED) | $(REPORTDIR) +ifneq ($(SPARQL_EXPORTS_ARGS),) + $(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS) +endif + +# ---------------------------------------- +# Release artefacts: export formats +# ---------------------------------------- + + +$(ONT)-full.obo: $(ONT)-full.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@ +$(ONT)-full.json: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +$(ONT)-base.obo: $(ONT)-base.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@ +$(ONT)-base.json: $(ONT)-base.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +# ---------------------------------------- +# Release artefacts: main release artefacts +# ---------------------------------------- + +$(ONT).owl: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert -o $@.tmp.owl && mv $@.tmp.owl $@ + +$(ONT).obo: $(ONT).owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@ +$(ONT).json: $(ONT).owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +# ----------------------------------------------------- +# Release artefacts: variants (base, full, simple, etc) +# ----------------------------------------------------- +SHARED_ROBOT_COMMANDS = + +$(ONTOLOGYTERMS): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/msio_terms.sparql $@ + +# ROBOT pipeline that merges imports, including components. +ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< + +# ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" +ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) + +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner $(REASONER) --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms false \ + relax $(RELAX_OPTIONS) \ + reduce -r $(REASONER) $(REDUCE_OPTIONS) \ + remove --base-iri $(URIBASE)/MSIO --axioms external --preserve-structure false --trim false \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ +# Full: The full artefacts with imports merged, reasoned. +$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner $(REASONER) --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ + relax $(RELAX_OPTIONS) \ + reduce -r $(REASONER) $(REDUCE_OPTIONS) \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ +# ---------------------------------------- +# Debugging Tools +# ---------------------------------------- + +explain_unsat: $(EDIT_PREPROCESSED) + $(ROBOT) explain -i $< -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/$@.md + + + +GHVERSION=v$(VERSION) + +.PHONY: public_release +public_release: + @test $(GHVERSION) + ls -alt $(RELEASE_ASSETS_AFTER_RELEASE) + gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes + +# ---------------------------------------- +# General Validation +# ---------------------------------------- +TSV= +ALL_TSV_FILES= + +validate-tsv: $(TSV) | $(TMPDIR) + for FILE in $< ; do \ + tsvalid $$FILE > $(TMPDIR)/validate.txt; \ + if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \ + done + +validate-all-tsv: $(ALL_TSV_FILES) + $(MAKE) validate-tsv TSV="$^" + +# ---------------------------------------- +# Editors Utilities +# ---------------------------------------- + +# This is an experimental target people that want to use ODK Extended Prefix Map (EPM) +# can use to pull the (currently inofficial) OBO EPM into the workspace. +# Users are instructed to refer to the EPM only through the variable $(EXTENDED_PREFIX_MAP) as +# its location might change in a feature version of ODK. +$(EXTENDED_PREFIX_MAP): /tools/obo.epm.json + cp $< $@ + + + +.PHONY: normalize_src +normalize_src: $(SRC) + $(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $< + +.PHONY: validate_idranges +validate_idranges: + if [ -f msio-idranges.owl ]; then \ + dicer-cli policy --assume-manchester --show-owlapi-error msio-idranges.owl ; \ + fi + +# Deprecated: Use 'sh run.sh odk.py update' without using the Makefile. +.PHONY: update_repo +update_repo: + odk.py update + + + +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. +.PHONY: clean +clean: + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done + rm -f $(CLEANFILES) + +.PHONY: help +help: + @echo "$$data" + +define data +Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command + +---------------------------------------- + Command reference +---------------------------------------- + +Core commands: +* prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports +* prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. +* update_repo: Update the ODK repository setup using the config file msio-odk.yaml (DEPRECATED) +* test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components +* odkversion: Show the current version of the ODK Makefile and ROBOT. +* clean: Delete all temporary files +* help: Print ODK Usage information +* public_release: Uploads the release file to a release management system, such as GitHub releases. Must be configured. + + +Imports management: +* refresh-imports: Refresh all imports and mirrors. +* recreate-components: Recreate all components. +* no-mirror-refresh-imports: Refresh all imports without downloading mirrors. +* refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'. +* refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'. +* no-mirror-refresh-%: Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'. +* mirror-%: Refresh a single mirror. + +Editor utilities: +* validate_idranges: Make sure your ID ranges file is formatted correctly +* normalize_src: Load and save your msio-edit file after you to make sure its serialised correctly +* explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes +* validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files +* validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. +* release_diff: Create a diff between the current release and the new release + +Additional build commands (advanced users) +* all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory. +* all_subsets: Build all subsets +* custom_reports: Generate all custom sparql reports you have configured in your msio-odk.yaml file. +* all_assets: Build all assets +* show_assets: Print a list of all assets that would be build by the release pipeline +* all_mappings: Update all SSSOM mapping sets + +Additional QC commands (advanced users) +* robot_reports: Run all configured ROBOT reports +* validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_msio-edit.owl. +* reason_test: Run a basic reasoning test + +Examples: +* sh run.sh make IMP=false prepare_release +* sh run.sh make test + +Tricks: +* To forcefully rebuild a target even if nothing has changed, either + invoke the 'clean' target (which will wipe out intermediate files) + or touch a file that your target depends on (typically the -edit file). +* Use the IMAGE parameter to the run.sh script to use a different image like odklite +* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging + +Updating the repository: +(to apply changes to the ODK configuration or switch to a newer ODK version) +* sh run.sh update_repo + +endef +export data + +include msio.Makefile \ No newline at end of file diff --git a/src/ontology/README-editors.md b/src/ontology/README-editors.md new file mode 100644 index 0000000..9c84a53 --- /dev/null +++ b/src/ontology/README-editors.md @@ -0,0 +1,27 @@ +These notes are for the EDITORS of msio + +This project was created using the [ontology development kit](https://github.com/INCATools/ontology-development-kit). See the site for details. + +For more details on ontology management, please see the +[OBO Academy Tutorials](https://oboacademy.github.io/obook/), the +[OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/) + +This documentation has been superceded by the ODK automatic documentation, which you can +activate by adding: + +``` +documentation: + documentation_system: mkdocs +``` + +to your Makefile and running: + +``` +sh run.sh make update_repo +``` +(Unix) + +``` +run.bat make update_repo +``` +(Windows) \ No newline at end of file diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml new file mode 100644 index 0000000..58525ae --- /dev/null +++ b/src/ontology/catalog-v001.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/src/ontology/imports/chebi_terms.txt b/src/ontology/imports/chebi_terms.txt new file mode 100644 index 0000000..d8847e2 --- /dev/null +++ b/src/ontology/imports/chebi_terms.txt @@ -0,0 +1,52 @@ +http://purl.obolibrary.org/obo/CHEBI_23367 +http://purl.obolibrary.org/obo/CHEBI_24431 +http://purl.obolibrary.org/obo/CHEBI_33839 +http://purl.obolibrary.org/obo/CHEBI_33696 +http://purl.obolibrary.org/obo/CHEBI_18059 +http://purl.obolibrary.org/obo/CHEBI_24432 +http://purl.obolibrary.org/obo/CHEBI_52206 +http://purl.obolibrary.org/obo/CHEBI_28659 +http://purl.obolibrary.org/obo/CHEBI_15377 +http://purl.obolibrary.org/obo/CHEBI_16991 +http://purl.obolibrary.org/obo/CHEBI_16670 +http://purl.obolibrary.org/obo/CHEBI_33250 +http://purl.obolibrary.org/obo/CHEBI_33697 +http://purl.obolibrary.org/obo/CHEBI_25212 +http://purl.obolibrary.org/obo/CHEBI_15956 +http://purl.obolibrary.org/obo/CHEBI_16134 +http://purl.obolibrary.org/obo/CHEBI_16227 +http://purl.obolibrary.org/obo/CHEBI_16737 +http://purl.obolibrary.org/obo/CHEBI_17137 +http://purl.obolibrary.org/obo/CHEBI_23116 +http://purl.obolibrary.org/obo/CHEBI_24913 +http://purl.obolibrary.org/obo/CHEBI_26078 +http://purl.obolibrary.org/obo/CHEBI_29236 +http://purl.obolibrary.org/obo/CHEBI_29237 +http://purl.obolibrary.org/obo/CHEBI_32954 +http://purl.obolibrary.org/obo/CHEBI_33819 +http://purl.obolibrary.org/obo/CHEBI_34856 +http://purl.obolibrary.org/obo/CHEBI_35255 +http://purl.obolibrary.org/obo/CHEBI_35895 +http://purl.obolibrary.org/obo/CHEBI_36601 +http://purl.obolibrary.org/obo/CHEBI_36928 +http://purl.obolibrary.org/obo/CHEBI_36931 +http://purl.obolibrary.org/obo/CHEBI_36934 +http://purl.obolibrary.org/obo/CHEBI_36938 +http://purl.obolibrary.org/obo/CHEBI_36940 +http://purl.obolibrary.org/obo/CHEBI_37968 +http://purl.obolibrary.org/obo/CHEBI_37971 +http://purl.obolibrary.org/obo/CHEBI_37974 +http://purl.obolibrary.org/obo/CHEBI_38472 +http://purl.obolibrary.org/obo/CHEBI_38589 +http://purl.obolibrary.org/obo/CHEBI_41981 +http://purl.obolibrary.org/obo/CHEBI_46324 +http://purl.obolibrary.org/obo/CHEBI_47032 +http://purl.obolibrary.org/obo/CHEBI_4705 +http://purl.obolibrary.org/obo/CHEBI_52451 +http://purl.obolibrary.org/obo/CHEBI_52634 +http://purl.obolibrary.org/obo/CHEBI_55317 +http://purl.obolibrary.org/obo/CHEBI_5692 +http://purl.obolibrary.org/obo/CHEBI_63005 +http://purl.obolibrary.org/obo/CHEBI_72544 +http://purl.obolibrary.org/obo/CHEBI_77701 +http://purl.obolibrary.org/obo/CHEBI_85060 \ No newline at end of file diff --git a/src/ontology/imports/chmo_terms.txt b/src/ontology/imports/chmo_terms.txt new file mode 100644 index 0000000..ad82a24 --- /dev/null +++ b/src/ontology/imports/chmo_terms.txt @@ -0,0 +1,42 @@ +http://purl.obolibrary.org/obo/CHMO_0000228 +http://purl.obolibrary.org/obo/CHMO_0000470 +http://purl.obolibrary.org/obo/CHMO_0000506 +http://purl.obolibrary.org/obo/CHMO_0001806 +http://purl.obolibrary.org/obo/CHMO_0001215 +http://purl.obolibrary.org/obo/CHMO_0000591 +http://purl.obolibrary.org/obo/CHMO_0000613 +http://purl.obolibrary.org/obo/CHMO_0000598 +http://purl.obolibrary.org/obo/CHMO_0000931 +http://purl.obolibrary.org/obo/CHMO_0001841 +http://purl.obolibrary.org/obo/CHMO_0000718 +http://purl.obolibrary.org/obo/CHMO_0000599 +http://purl.obolibrary.org/obo/CHMO_0001844 +http://purl.obolibrary.org/obo/CHMO_0001864 +http://purl.obolibrary.org/obo/CHMO_0000600 +http://purl.obolibrary.org/obo/CHMO_0000592 +http://purl.obolibrary.org/obo/CHMO_0000575 +http://purl.obolibrary.org/obo/CHMO_0000497 +http://purl.obolibrary.org/obo/CHMO_0000514 +http://purl.obolibrary.org/obo/CHMO_0000524 +http://purl.obolibrary.org/obo/CHMO_0000571 +http://purl.obolibrary.org/obo/CHMO_0000593 +http://purl.obolibrary.org/obo/CHMO_0000595 +http://purl.obolibrary.org/obo/CHMO_0000605 +http://purl.obolibrary.org/obo/CHMO_0000606 +http://purl.obolibrary.org/obo/CHMO_0000607 +http://purl.obolibrary.org/obo/CHMO_0000719 +http://purl.obolibrary.org/obo/CHMO_0001150 +http://purl.obolibrary.org/obo/CHMO_0001195 +http://purl.obolibrary.org/obo/CHMO_0001852 +http://purl.obolibrary.org/obo/CHMO_0001862 +http://purl.obolibrary.org/obo/CHMO_0001863 +http://purl.obolibrary.org/obo/CHMO_0001865 +http://purl.obolibrary.org/obo/CHMO_0001866 +http://purl.obolibrary.org/obo/CHMO_0001867 +http://purl.obolibrary.org/obo/CHMO_0001868 +http://purl.obolibrary.org/obo/CHMO_0001869 +http://purl.obolibrary.org/obo/CHMO_0002060 +http://purl.obolibrary.org/obo/CHMO_0002301 +http://purl.obolibrary.org/obo/CHMO_0002380 +http://purl.obolibrary.org/obo/CHMO_0002442 +http://purl.obolibrary.org/obo/CHMO_0002867 \ No newline at end of file diff --git a/src/ontology/imports/cl_terms.txt b/src/ontology/imports/cl_terms.txt new file mode 100644 index 0000000..3a08965 --- /dev/null +++ b/src/ontology/imports/cl_terms.txt @@ -0,0 +1,3 @@ +http://purl.obolibrary.org/obo/CL_0000000 +http://purl.obolibrary.org/obo/CL_0000578 +http://purl.obolibrary.org/obo/CL_0000010 \ No newline at end of file diff --git a/src/ontology/imports/duo_terms.txt b/src/ontology/imports/duo_terms.txt new file mode 100644 index 0000000..68f26bd --- /dev/null +++ b/src/ontology/imports/duo_terms.txt @@ -0,0 +1,25 @@ +http://purl.obolibrary.org/obo/DUO_0000001 +http://purl.obolibrary.org/obo/DUO_0000002 +http://purl.obolibrary.org/obo/DUO_0000003 +http://purl.obolibrary.org/obo/DUO_0000017 +http://purl.obolibrary.org/obo/DUO_0000010 +http://purl.obolibrary.org/obo/DUO_0000004 +http://purl.obolibrary.org/obo/DUO_0000005 +http://purl.obolibrary.org/obo/DUO_0000006 +http://purl.obolibrary.org/obo/DUO_0000007 +http://purl.obolibrary.org/obo/DUO_0000011 +http://purl.obolibrary.org/obo/DUO_0000012 +http://purl.obolibrary.org/obo/DUO_0000014 +http://purl.obolibrary.org/obo/DUO_0000015 +http://purl.obolibrary.org/obo/DUO_0000016 +http://purl.obolibrary.org/obo/DUO_0000018 +http://purl.obolibrary.org/obo/DUO_0000019 +http://purl.obolibrary.org/obo/DUO_0000020 +http://purl.obolibrary.org/obo/DUO_0000021 +http://purl.obolibrary.org/obo/DUO_0000022 +http://purl.obolibrary.org/obo/DUO_0000024 +http://purl.obolibrary.org/obo/DUO_0000025 +http://purl.obolibrary.org/obo/DUO_0000026 +http://purl.obolibrary.org/obo/DUO_0000027 +http://purl.obolibrary.org/obo/DUO_0000028 +http://purl.obolibrary.org/obo/DUO_0000029 \ No newline at end of file diff --git a/src/ontology/imports/gaz_terms.txt b/src/ontology/imports/gaz_terms.txt new file mode 100644 index 0000000..cea9fac --- /dev/null +++ b/src/ontology/imports/gaz_terms.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/GAZ_00000448 diff --git a/src/ontology/imports/go_terms.txt b/src/ontology/imports/go_terms.txt new file mode 100644 index 0000000..ec137aa --- /dev/null +++ b/src/ontology/imports/go_terms.txt @@ -0,0 +1,5 @@ +http://purl.obolibrary.org/obo/GO_0003674 +http://purl.obolibrary.org/obo/GO_0008150 +http://purl.obolibrary.org/obo/GO_0043234 +http://purl.obolibrary.org/obo/GO_0003824 +http://purl.obolibrary.org/obo/GO_0010467 \ No newline at end of file diff --git a/src/ontology/imports/iao_terms.txt b/src/ontology/imports/iao_terms.txt new file mode 100644 index 0000000..ba61622 --- /dev/null +++ b/src/ontology/imports/iao_terms.txt @@ -0,0 +1,84 @@ +http://purl.obolibrary.org/obo/IAO_0000030 +http://purl.obolibrary.org/obo/IAO_0000027 +http://purl.obolibrary.org/obo/IAO_0000078 +http://purl.obolibrary.org/obo/IAO_0000102 +http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000232 +http://purl.obolibrary.org/obo/IAO_0000119 +http://purl.obolibrary.org/obo/IAO_0000111 +http://purl.obolibrary.org/obo/IAO_0000114 +http://purl.obolibrary.org/obo/IAO_0000117 +http://purl.obolibrary.org/obo/IAO_0000112 +http://purl.obolibrary.org/obo/IAO_0000116 +http://purl.obolibrary.org/obo/IAO_0000118 +http://purl.obolibrary.org/obo/IAO_0000412 +http://purl.obolibrary.org/obo/IAO_0000600 +http://purl.obolibrary.org/obo/IAO_0000601 +http://purl.obolibrary.org/obo/IAO_0000602 +http://purl.obolibrary.org/obo/IAO_0010000 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+http://purl.obolibrary.org/obo/IAO_0000416 +http://purl.obolibrary.org/obo/IAO_0000582 +http://purl.obolibrary.org/obo/IAO_0000002 +http://purl.obolibrary.org/obo/IAO_0000120 +http://purl.obolibrary.org/obo/IAO_0000121 +http://purl.obolibrary.org/obo/IAO_0000122 +http://purl.obolibrary.org/obo/IAO_0000123 +http://purl.obolibrary.org/obo/IAO_0000124 +http://purl.obolibrary.org/obo/IAO_0000125 +http://purl.obolibrary.org/obo/IAO_0000423 +http://purl.obolibrary.org/obo/IAO_0000428 +http://purl.obolibrary.org/obo/IAO_0000064 +http://purl.obolibrary.org/obo/IAO_0000101 +http://purl.obolibrary.org/obo/IAO_0000226 +http://purl.obolibrary.org/obo/IAO_0000227 +http://purl.obolibrary.org/obo/IAO_0000228 +http://purl.obolibrary.org/obo/IAO_0000229 +http://purl.obolibrary.org/obo/IAO_0000039 +http://purl.obolibrary.org/obo/IAO_0000004 +http://purl.obolibrary.org/obo/IAO_0000219 +http://purl.obolibrary.org/obo/IAO_0000407 +http://purl.obolibrary.org/obo/IAO_0000404 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+Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(Datatype(rdf:PlainLiteral)) +Declaration(Datatype(rdfs:Literal)) +Declaration(Datatype(xsd:float)) +############################ +# Annotation Properties +############################ + +# Annotation Property: (editor preferred term) + +AnnotationAssertion( "editor preferred term"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor preferred term"@en) + +# Annotation Property: (example of usage) + +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "example of usage"@en) + +# Annotation Property: (has curation status) + +AnnotationAssertion( "has curation status"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "has curation status"@en) + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition"@en) + +# Annotation Property: (editor note) + +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (alternative label) + +AnnotationAssertion( "alternative label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) +AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "alternative label"@en) +AnnotationAssertion(rdfs:label "alternative term"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (curator note) + +AnnotationAssertion( "curator note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "curator note"@en) + +# Annotation Property: (imported from) + +AnnotationAssertion( "imported from"@en) +AnnotationAssertion( ) +AnnotationAssertion( "For external terms/classes, the ontology from which the term was imported"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "imported from"@en) + +# Annotation Property: (elucidation) + +AnnotationAssertion( "elucidation"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Barry Smith"@en) +AnnotationAssertion( "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en) +AnnotationAssertion(rdfs:label "elucidation"@en) + +# Annotation Property: (has associated axiom(nl)) + +AnnotationAssertion( "has associated axiom(nl)"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "An axiom associated with a term expressed using natural language"@en) +AnnotationAssertion(rdfs:label "has associated axiom(nl)"@en) + +# Annotation Property: (has associated axiom(fol)) + +AnnotationAssertion( "has associated axiom(fol)"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "An axiom expressed in first order logic using CLIF syntax"@en) +AnnotationAssertion(rdfs:label "has associated axiom(fol)"@en) + +# Annotation Property: (has axiom label) + +AnnotationAssertion( "has axiom id"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI"@en) +AnnotationAssertion(rdfs:label "has axiom label"@en) + +# Annotation Property: (temporal interpretation) + +AnnotationAssertion( "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") +AnnotationAssertion(rdfs:label "temporal interpretation") +AnnotationAssertion(rdfs:label "temporal interpretation"@en) + +# Annotation Property: (Contributor) + +AnnotationAssertion(rdfs:label "Contributor") + +# Annotation Property: (Creator) + +AnnotationAssertion(rdfs:label "Creator") + +# Annotation Property: (Description) + +AnnotationAssertion(rdfs:label "Description") + +# Annotation Property: (Resource Identifier) + +AnnotationAssertion(rdfs:label "Resource Identifier") + +# Annotation Property: (Language) + +AnnotationAssertion(rdfs:label "Language") + +# Annotation Property: (Publisher) + +AnnotationAssertion(rdfs:label "Publisher") + +# Annotation Property: (Relation) + +AnnotationAssertion(rdfs:label "Relation") + +# Annotation Property: (Rights Management) + +AnnotationAssertion(rdfs:label "Rights Management") + +# Annotation Property: (Title) + +AnnotationAssertion(rdfs:label "Title") + +# Annotation Property: (Resource Type) + +AnnotationAssertion(rdfs:label "Resource Type") + +# Annotation Property: (shorthand) + +AnnotationAssertion(rdfs:label "shorthand") + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion( "has_part") +AnnotationAssertion( "has_part") +AnnotationAssertion(rdfs:label "has part") +AnnotationAssertion(rdfs:label "has part"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"@en) +AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (preceded by) + +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion(rdfs:label "preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion(rdfs:label "precedes"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (probes_atom) + +AnnotationAssertion( "CHMO:0002922") +AnnotationAssertion(rdfs:label "probes_atom") + +# Object Property: (lacks_plasma_membrane_part) + +AnnotationAssertion(rdfs:label "lacks_plasma_membrane_part") + +# Object Property: (is restricted to) + +AnnotationAssertion( "A is restricted to B iff A is a consent code and B is an investigation and A may only participate in instances of a class C, of which B is an instance.") +AnnotationAssertion( "J. Neil Otte") +AnnotationAssertion( "E.g. A dataset is restricted to an instance of an investigation for a specific disease or at geographical location.") +AnnotationAssertion( "DUO:0000010") +AnnotationAssertion(rdfs:label "is restricted to") + +# Object Property: (has measurement unit label) + +AnnotationAssertion(rdfs:label "has measurement unit label"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (is about) + +AnnotationAssertion( "This document is about information artifacts and their representations"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (denotes) + +AnnotationAssertion( "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named."@en) +AnnotationAssertion( "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically"@en) +AnnotationAssertion( "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"@en) +AnnotationAssertion(rdfs:label "denotes"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is quality measurement of) + +AnnotationAssertion( "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q"@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later"@en) +AnnotationAssertion( "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] + +This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details. +-- +From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] + +unit of measure is a quality, e.g. the length of a ruler. + +[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] + +[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] + +a represents b means either a denotes b or a describes + +describe: +a describes b means a is about b and a allows an inference of at least one quality of b + +We have had a long discussion about denotes versus describes."@en) +AnnotationAssertion( "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. + +a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality."@en) +AnnotationAssertion( "From the second meeting on IAO: + +An attempt at defining assay using Barry's \"reliability\" wording + +assay: +process and has_input some material entity +and has_output some information content entity +and which is such that instances of this process type reliably generate +outputs that describes the input."@en) +AnnotationAssertion( "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is quality measurement of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (denoted by) + +AnnotationAssertion( "inverse of the relation 'denotes'"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"@en) +AnnotationAssertion(rdfs:label "denoted by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has coordinate unit label) + +AnnotationAssertion(rdfs:label "has coordinate unit label"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is duration of) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a process to a time-measurement-datum that represents the duration of the process"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is duration of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is quality measured as) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of the relation of is quality measurement of"@en) +AnnotationAssertion( "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is quality measured as"@en) + +# Object Property: (has time stamp) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "has time stamp"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a time stamped measurement datum to the measurement datum that was measured"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "has measurement datum"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (is_supported_by_data) + +AnnotationAssertion( "The relation between the conclusion \"Gene tpbA is involved in EPS production\" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.") +AnnotationAssertion( ) +AnnotationAssertion( "The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process"@en) +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion( "Philly 2011 workshop") +AnnotationAssertion(rdfs:label "is_supported_by_data") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has_specified_input) + +AnnotationAssertion( "has specified input") +AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is specified input of"@en) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has specified input"@en) +AnnotationAssertion(rdfs:label "has_specified_input"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is specified input of) + +AnnotationAssertion( "is specified input of") +AnnotationAssertion( "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is specified input of"@en) +AnnotationAssertion(rdfs:label "is_specified_input_of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has_specified_output) + +AnnotationAssertion( "has specified output") +AnnotationAssertion( "has_specified_output") +AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is specified output of"@en) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has specified output"@en) +AnnotationAssertion(rdfs:label "has_specified_output"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is_specified_output_of) + +AnnotationAssertion( "is specified output of") +AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is specified output of"@en) +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (achieves_planned_objective) + +AnnotationAssertion( "achieves_planned_objective") +AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process."@en) +AnnotationAssertion( "BP, AR, PPPB branch") +AnnotationAssertion( "PPPB branch derived") +AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has grain) + +AnnotationAssertion( "has grain") +AnnotationAssertion( "the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car."@en) +AnnotationAssertion( "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349") +AnnotationAssertion(rdfs:label "has grain") +SubObjectPropertyOf( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "objective_achieved_by") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process."@en) +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has value specification) + +AnnotationAssertion( ) +AnnotationAssertion( "A relation between an information content entity and a value specification that specifies its value."@en) +AnnotationAssertion( "PERSON: James A. Overton") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has value specification") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (has characteristic) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "has_participant") +AnnotationAssertion( "has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is concretized as) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +ObjectPropertyRange( ObjectUnionOf( )) + +# Object Property: (concretizes) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyDomain( ObjectUnionOf( )) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion( "has_role") +AnnotationAssertion( "has_role") +AnnotationAssertion(rdfs:label "has role") +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (derives from) + +AnnotationAssertion( "this cell derives from this parent cell (cell division)"@en) +AnnotationAssertion( "this nucleus derives from this parent nucleus (nuclear division)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) +AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'."@en) +AnnotationAssertion( "derives_from"@en) +AnnotationAssertion( "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.") +AnnotationAssertion(rdfs:label "derives from"@en) +InverseObjectProperties( ) + +# Object Property: (derives into) + +AnnotationAssertion( "this parent cell derives into this cell (cell division)"@en) +AnnotationAssertion( "this parent nucleus derives into this nucleus (nuclear division)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) +AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'."@en) +AnnotationAssertion( "derives_into"@en) +AnnotationAssertion(rdfs:label "derives into"@en) + +# Object Property: (ends after) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( ) +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( ) +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion(rdfs:label "immediately precedes"@en) +SubObjectPropertyOf( ) + +# Object Property: (has plasma membrane part) + +AnnotationAssertion( "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has plasma membrane part"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "overlaps"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (only in taxon) + +AnnotationAssertion( "lactation SubClassOf 'only in taxon' some 'Mammalia'") +AnnotationAssertion( ) +AnnotationAssertion( "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.") +AnnotationAssertion( "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "only in taxon") +SubObjectPropertyOf( ) + +# Object Property: (in taxon) + +AnnotationAssertion( ) +AnnotationAssertion( "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "in taxon") +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (develops from) + +AnnotationAssertion( ) +AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "develops from"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (develops into) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of develops from") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "develops into"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (regulates) + +AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "regulates"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( ) +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion(rdfs:label "capable of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( ) +AnnotationAssertion( "has function in") +AnnotationAssertion(rdfs:label "capable of part of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (starts) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of starts with") +AnnotationAssertion( ) +AnnotationAssertion( "Allen") +AnnotationAssertion(rdfs:label "starts"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (starts with) + +AnnotationAssertion( "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor") +AnnotationAssertion( ) +AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +AnnotationAssertion( ) +AnnotationAssertion( "started by") +AnnotationAssertion(rdfs:label "starts with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (ends) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of ends with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ends"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (ends with) + +AnnotationAssertion( ) +AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +AnnotationAssertion( ) +AnnotationAssertion( "finished by") +AnnotationAssertion(rdfs:label "ends with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion( ) +AnnotationAssertion( "consumes") +AnnotationAssertion(rdfs:label "has input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (has output) + +AnnotationAssertion( ) +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion( ) +AnnotationAssertion( "produces") +AnnotationAssertion(rdfs:label "has output"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has developmental contribution from) + +AnnotationAssertion( "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]") +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has developmental contribution from"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (developmentally contributes to) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of has developmental contribution from") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmentally contributes to"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (developmentally preceded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( "In general you should not use this relation to make assertions - use one of the more specific relations below this one") +AnnotationAssertion(rdfs:label "developmentally preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (developmentally succeeded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Inverse of developmentally preceded by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) +SubObjectPropertyOf( ) + +# Object Property: (results in developmental progression of) + +AnnotationAssertion( ) +AnnotationAssertion( "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).") +AnnotationAssertion( "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "results in developmental progression of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (results in development of) + +AnnotationAssertion( "every flower development (GO:0009908) results in development of some flower (PO:0009046)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.") +AnnotationAssertion( ) +AnnotationAssertion( "http://www.geneontology.org/GO.doc.development.shtml"^^xsd:anyURI) +AnnotationAssertion(rdfs:label "results in development of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in formation of anatomical entity) + +AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") +AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "GOC:mtg_berkeley_2013") +AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (results in morphogenesis of) + +AnnotationAssertion( "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.") +AnnotationAssertion( "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.") +AnnotationAssertion( ) +AnnotationAssertion( "GOC:mtg_berkeley_2013") +AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (characteristic of part of) + +AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") +AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") +AnnotationAssertion( ) +AnnotationAssertion( "inheres in part of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of part of"@en) +SubObjectPropertyOf( ) + +# Object Property: (results in acquisition of features of) + +AnnotationAssertion( "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.") +AnnotationAssertion( "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity") +AnnotationAssertion( ) +AnnotationAssertion( "GOC:mtg_berkeley_2013") +AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (evolutionarily related to) + +AnnotationAssertion( "A relationship that holds via some environmental process") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.") +AnnotationAssertion(rdfs:label "evolutionarily related to"@en) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (developmentally related to) + +AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") +AnnotationAssertion(rdfs:label "developmentally related to"@en) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion(rdfs:label "functionally related to"@en) + +# Object Property: (part of structure that is capable of) + +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +AnnotationAssertion( ) +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) +IrreflexiveObjectProperty() + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (output of) + +AnnotationAssertion( "inverse of has output") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "output of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (formed as result of) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "formed as result of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has developmental potential involving) + +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has developmental potential involving"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has potential to developmentally contribute to) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has the potential to develop into y iff x develops into y or if x is capable of developing into y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to directly develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causally related to) + +AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (provides input for) + +AnnotationAssertion( "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.") +AnnotationAssertion( ) +AnnotationAssertion( "directly provides input for") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "provides input for"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (transitively provides input for) + +AnnotationAssertion( ) +AnnotationAssertion( "transitive form of directly_provides_input_for") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.") +AnnotationAssertion(rdfs:label "transitively provides input for"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( ) +AnnotationAssertion( "influences (processual)") +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (depends on) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "depends on") + +# Object Property: (has part structure that is capable of) + +AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") +AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part structure that is capable of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in breakdown of) + +AnnotationAssertion( "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p") +AnnotationAssertion(rdfs:label "results in breakdown of") +SubObjectPropertyOf( ) + +# Object Property: (results in assembly of) + +AnnotationAssertion(rdfs:label "results in assembly of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in disassembly of) + +AnnotationAssertion(rdfs:label "results in disassembly of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in organization of) + +AnnotationAssertion( "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c") +AnnotationAssertion(rdfs:label "results in organization of") +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (has primary input or output) + +AnnotationAssertion( "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.") +AnnotationAssertion(rdfs:label "has primary input or output") +SubObjectPropertyOf( ) + +# Object Property: (has primary output) + +AnnotationAssertion(rdfs:label "has primary output") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has primary input) + +AnnotationAssertion(rdfs:label "has primary input") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +SubObjectPropertyOf( ) + +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") +AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion(rdfs:label "realized in response to"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (generically depends on) + +AnnotationAssertion( "Genetic information generically depend on molecules of DNA.") +AnnotationAssertion( "The novel *War and Peace* generically depends on this copy of the novel.") +AnnotationAssertion( "The pattern shared by chess boards generically depends on any chess board.") +AnnotationAssertion( "The score of a symphony g-depends on a copy of the score.") +AnnotationAssertion( "This pdf file generically depends on this server.") +AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "generically depends on") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is carrier of) + +AnnotationAssertion( "Molecules of DNA are carriers of genetic information.") +AnnotationAssertion( "This copy of *War and Peace* is carrier of the novel written by Tolstoy.") +AnnotationAssertion( "This hard drive is carrier of these data items.") +AnnotationAssertion( "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "is carrier of"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (device utilizes material) + +AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") +AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") +AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion(rdfs:label "device utilizes material"@en) + +# Object Property: (is anatomical entity) + +AnnotationAssertion( "This property only applies to anatomical entities.") +AnnotationAssertion(rdfs:label "is anatomical entity") +ObjectPropertyDomain( ) + +# Object Property: (results in changes to anatomical or cellular structure) + +AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") +AnnotationAssertion(rdfs:label "results in changes to anatomical or cellular structure") +SubObjectPropertyOf( ) + +# Object Property: (has functional parent) + +AnnotationAssertion( "has_functional_parent") +AnnotationAssertion(rdfs:label "has functional parent") + +# Object Property: (has parent hydride) + +AnnotationAssertion( "has_parent_hydride") +AnnotationAssertion(rdfs:label "has parent hydride") + +# Object Property: (is conjugate acid of) + +AnnotationAssertion( "is_conjugate_acid_of") +AnnotationAssertion(rdfs:label "is conjugate acid of") +InverseObjectProperties( ) + +# Object Property: (is conjugate base of) + +AnnotationAssertion( "is_conjugate_base_of") +AnnotationAssertion(rdfs:label "is conjugate base of") + +# Object Property: (is substituent group from) + +AnnotationAssertion( "is_substituent_group_from") +AnnotationAssertion(rdfs:label "is substituent group from") + +# Object Property: (is tautomer of) + +AnnotationAssertion( "is_tautomer_of") +AnnotationAssertion(rdfs:label "is tautomer of") +TransitiveObjectProperty() + + +############################ +# Data Properties +############################ + +# Data Property: (has measurement value) + +AnnotationAssertion(rdfs:label "has measurement value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:double) + +# Data Property: (has x coordinate value) + +AnnotationAssertion(rdfs:label "has x coordinate value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:float) + +# Data Property: (has y coordinate value) + +AnnotationAssertion(rdfs:label "has y coordinate value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:float) + +# Data Property: (has specified numeric value) + +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a value specification and a number that quantifies it."@en) +AnnotationAssertion( "A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.") +AnnotationAssertion( "PERSON: James A. Overton") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has specified numeric value") +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( owl:real) + +# Data Property: (has specified value) + +AnnotationAssertion( "A relation between a value specification and a literal."@en) +AnnotationAssertion( "This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has specified value"@en) +DataPropertyDomain( ) + + + +############################ +# Classes +############################ + +# Class: (integer32) + +AnnotationAssertion(rdfs:label "integer32"@en) +SubClassOf( ) + +# Class: (sample number) + +AnnotationAssertion( "NMR:1000001") +AnnotationAssertion(rdfs:label "sample number") +SubClassOf( ) + +# Class: (long64) + +AnnotationAssertion(rdfs:label "long64"@en) +SubClassOf( ) + +# Class: (sample state information) + +AnnotationAssertion( "NMR:1000003") +AnnotationAssertion(rdfs:label "sample state information") +SubClassOf( ) + +# Class: (sample mass information) + +AnnotationAssertion( "NMR:1000004") +AnnotationAssertion(rdfs:label "sample mass information") +SubClassOf( ) + +# Class: (sample volume) + +AnnotationAssertion( "NMR:1000005") +AnnotationAssertion(rdfs:label "sample volume") +SubClassOf( ) + +# Class: (sample concentration) + +AnnotationAssertion( "NMR:1000006") +AnnotationAssertion(rdfs:label "sample concentration") +SubClassOf( ) + +# Class: (quadrature detection) + +AnnotationAssertion(rdfs:label "quadrature detection"@en) +SubClassOf( ) + +# Class: (contact role) + +AnnotationAssertion(rdfs:label "contact role"@en) +SubClassOf( ) + +# Class: (data file attribute) + +AnnotationAssertion(rdfs:label "data file attribute"@en) +SubClassOf( ) + +# Class: (NMR instrument type) + +AnnotationAssertion(rdfs:label "NMR instrument type"@en) +SubClassOf( ) + +# Class: (1D spectrum coordinate system descriptor) + +AnnotationAssertion(rdfs:label "1D spectrum coordinate system descriptor"@en) +SubClassOf( ) + +# Class: (pre-acquisition solvent suppression) + +AnnotationAssertion(rdfs:label "pre-acquisition solvent suppression"@en) +SubClassOf( ) + +# Class: (peak processing) + +AnnotationAssertion(rdfs:label "peak processing"@en) +SubClassOf( ) + +# Class: (Hexafluorobenzene) + +AnnotationAssertion(rdfs:label "Hexafluorobenzene"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (Chloroform-d) + +AnnotationAssertion(rdfs:label "Chloroform-d"@en) +SubClassOf( ) + +# Class: (heavy water) + +AnnotationAssertion(rdfs:label "heavy water"@en) +SubClassOf( ) + +# Class: (sample pH) + +AnnotationAssertion(rdfs:label "sample pH"@en) +SubClassOf( ) + +# Class: (post buffer pH) + +AnnotationAssertion(rdfs:label "post buffer pH"@en) +SubClassOf( ) + +# Class: (apodization) + +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf") +AnnotationAssertion(rdfs:label "apodization") +SubClassOf( ) + +# Class: (metabolomics database identifier) + +AnnotationAssertion(rdfs:label "metabolomics database identifier"@en) +SubClassOf( ) + +# Class: (Metabolights identifier) + +AnnotationAssertion(rdfs:label "Metabolights identifier"@en) +SubClassOf( ) + +# Class: (acetonitrile) + +AnnotationAssertion(rdfs:label "acetonitrile"@en) +SubClassOf( ) + +# Class: (1,4-Dioxane) + +AnnotationAssertion(rdfs:label "1,4-Dioxane"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (1H spectrum reference compound) + +AnnotationAssertion(rdfs:label "1H spectrum reference compound"@en) +SubClassOf( ) + +# Class: (2,2-Dimethyl-2-silapentane-5-sulfonate) + +AnnotationAssertion(rdfs:label "2,2-Dimethyl-2-silapentane-5-sulfonate"@en) +SubClassOf( ) + +# Class: (sodium acetate) + +AnnotationAssertion(rdfs:label "sodium acetate"@en) +SubClassOf( ) + +# Class: (tetramethylsilane) + +AnnotationAssertion(rdfs:label "tetramethylsilane"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (13C spectrum reference compound) + +AnnotationAssertion(rdfs:label "13C spectrum reference compound"@en) +SubClassOf( ) + +# Class: (NMR instrument model) + +AnnotationAssertion( "NMR:1000031") +AnnotationAssertion(rdfs:label "NMR instrument model") +SubClassOf( ) + +# Class: (instrument customization) + +AnnotationAssertion( "NMR:1000032") +AnnotationAssertion(rdfs:label "instrument customization") +SubClassOf( ) + +# Class: (Chloroform-d1) + +AnnotationAssertion(rdfs:label "Chloroform-d1"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (keyword) + +AnnotationAssertion(rdfs:label "keyword") +SubClassOf( ) + +# Class: (tetramethylammonium bromide) + +AnnotationAssertion(rdfs:label "tetramethylammonium bromide"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (15N spectrum reference compound) + +AnnotationAssertion(rdfs:label "15N spectrum reference compound"@en) +SubClassOf( ) + +# Class: (ammonia (liquid)) + +AnnotationAssertion(rdfs:label "ammonia (liquid)"@en) +SubClassOf( ) + +# Class: (ammonium bromide) + +AnnotationAssertion(rdfs:label "ammonium bromide"@en) +SubClassOf( ) + +# Class: (1,4-morpholine) + +AnnotationAssertion(rdfs:label "1,4-morpholine"@en) +SubClassOf( ) + +# Class: (nitromethane) + +AnnotationAssertion(rdfs:label "nitromethane"@en) +SubClassOf( ) + +# Class: (pyridine) + +AnnotationAssertion(rdfs:label "pyridine"@en) +SubClassOf( ) + +# Class: (sodium nitrate) + +AnnotationAssertion(rdfs:label "sodium nitrate"@en) +SubClassOf( ) + +# Class: (post-acquisition solvent suppression) + +AnnotationAssertion(rdfs:label "post-acquisition solvent suppression"@en) +SubClassOf( ) + +# Class: (decoupling method) + +AnnotationAssertion( "Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.") +AnnotationAssertion(rdfs:label "decoupling method"@en) +SubClassOf( ) + +# Class: (homonuclear decoupling) + +AnnotationAssertion(rdfs:label "homonuclear decoupling"@en) +SubClassOf( ) + +# Class: (heteronuclear decoupling) + +AnnotationAssertion(rdfs:label "heteronuclear decoupling"@en) +SubClassOf( ) + +# Class: (emulsion) + +AnnotationAssertion( "NMR:1000047") +AnnotationAssertion(rdfs:label "emulsion") +SubClassOf( ) + +# Class: (gas) + +AnnotationAssertion( "NMR:1000048") +AnnotationAssertion(rdfs:label "gas") +SubClassOf( ) + +# Class: (liquid) + +AnnotationAssertion( "NMR:1000049") +AnnotationAssertion(rdfs:label "liquid") +SubClassOf( ) + +# Class: (solid) + +AnnotationAssertion( "NMR:1000050") +AnnotationAssertion(rdfs:label "solid") +SubClassOf( ) + +# Class: (solution) + +AnnotationAssertion( "NMR:1000051") +AnnotationAssertion(rdfs:label "solution") +SubClassOf( ) + +# Class: (suspension) + +AnnotationAssertion( "NMR:1000052") +AnnotationAssertion(rdfs:label "suspension") +SubClassOf( ) + +# Class: (sample batch information) + +AnnotationAssertion( "NMR:1000053") +AnnotationAssertion(rdfs:label "sample batch information") +SubClassOf( ) + +# Class: (broad band decoupling) + +AnnotationAssertion(rdfs:label "broad band decoupling"@en) +SubClassOf( ) + +# Class: (off resonance decoupling) + +AnnotationAssertion(rdfs:label "off resonance decoupling"@en) +SubClassOf( ) + +# Class: (specific decoupling) + +AnnotationAssertion(rdfs:label "specific decoupling"@en) +SubClassOf( ) + +# Class: (angle of sinusoid) + +AnnotationAssertion(rdfs:label "angle of sinusoid"@en) +SubClassOf( ) + +# Class: (31P spectrum reference compound) + +AnnotationAssertion(rdfs:label "31P spectrum reference compound"@en) +SubClassOf( ) + +# Class: (phosphoric acid) + +AnnotationAssertion(rdfs:label "phosphoric acid"@en) +SubClassOf( ) + +# Class: (phosphorus) + +AnnotationAssertion(rdfs:label "phosphorus"@en) +SubClassOf( ) + +# Class: (trimethyl phosphate) + +AnnotationAssertion(rdfs:label "trimethyl phosphate"@en) +SubClassOf( ) + +# Class: (triphenylphosphine) + +AnnotationAssertion(rdfs:label "triphenylphosphine"@en) +SubClassOf( ) + +# Class: (triphenylphosphine oxide) + +AnnotationAssertion(rdfs:label "triphenylphosphine oxide"@en) +SubClassOf( ) + +# Class: (co-dissolved internal reference) + +AnnotationAssertion(rdfs:label "co-dissolved internal reference"@en) +SubClassOf( ) + +# Class: (synthetic reference signal) + +AnnotationAssertion(rdfs:label "synthetic reference signal"@en) +SubClassOf( ) + +# Class: (residual solvent signal) + +AnnotationAssertion(rdfs:label "residual solvent signal"@en) +SubClassOf( ) + +# Class: (FID zero filling) + +AnnotationAssertion(rdfs:label "FID zero filling"@en) +SubClassOf( ) + +# Class: (data extrapolation using linear prediction) + +AnnotationAssertion(rdfs:label "data extrapolation using linear prediction"@en) +SubClassOf( ) + +# Class: (multiplying FID by window function) + +AnnotationAssertion(rdfs:label "multiplying FID by window function"@en) +SubClassOf( ) + +# Class: (FID fourier transformation) + +AnnotationAssertion(rdfs:label "FID fourier transformation"@en) +SubClassOf( ) + +# Class: (phase correction) + +AnnotationAssertion(rdfs:label "phase correction"@en) +SubClassOf( ) + +# Class: (peak integration) + +AnnotationAssertion(rdfs:label "peak integration"@en) +SubClassOf( ) + +# Class: (peak alignment) + +AnnotationAssertion(rdfs:label "peak alignment"@en) +SubClassOf( ) + +# Class: (peak shape fitting) + +AnnotationAssertion(rdfs:label "peak shape fitting"@en) +SubClassOf( ) + +# Class: (spectral referencing) + +AnnotationAssertion(rdfs:label "spectral referencing"@en) +SubClassOf( ) + +# Class: (sodium trimethylsilyl-propionate) + +AnnotationAssertion(rdfs:label "sodium trimethylsilyl-propionate"@en) +SubClassOf( ) + +# Class: (linear scaling) + +AnnotationAssertion(rdfs:label "linear scaling"@en) +SubClassOf( ) + +# Class: (scaling) + +AnnotationAssertion(rdfs:label "scaling"@en) +SubClassOf( ) + +# Class: (non-linear scaling) + +AnnotationAssertion(rdfs:label "non-linear scaling"@en) +SubClassOf( ) + +# Class: (total spectral area scaling) + +AnnotationAssertion(rdfs:label "total spectral area scaling"@en) +SubClassOf( ) + +# Class: (probabilistic quotient normalization) + +AnnotationAssertion(rdfs:label "probabilistic quotient normalization"@en) +SubClassOf( ) + +# Class: (scaling by generalized logarithmic transformation) + +AnnotationAssertion(rdfs:label "scaling by generalized logarithmic transformation"@en) +SubClassOf( ) + +# Class: (pareto scaling) + +AnnotationAssertion(rdfs:label "pareto scaling"@en) +SubClassOf( ) + +# Class: (autoscaling) + +AnnotationAssertion(rdfs:label "autoscaling"@en) +SubClassOf( ) + +# Class: (2D J-resolved spectrum) + +AnnotationAssertion(rdfs:label "2D J-resolved spectrum"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (MetaboLab software) + +AnnotationAssertion(rdfs:label "MetaboLab software"@en) +SubClassOf( ) + +# Class: (Metaboquant software) + +AnnotationAssertion(rdfs:label "Metaboquant software"@en) +SubClassOf( ) + +# Class: (rNMR software) + +AnnotationAssertion(rdfs:label "rNMR software"@en) +SubClassOf( ) + +# Class: (open source NMR software) + +AnnotationAssertion(rdfs:label "open source NMR software"@en) +SubClassOf( ) + +# Class: (commercial NMR software) + +AnnotationAssertion(rdfs:label "commercial NMR software"@en) +SubClassOf( ) + +# Class: (NMRLab software) + +AnnotationAssertion(rdfs:label "NMRLab software"@en) +SubClassOf( ) + +# Class: (NMRPipe software) + +AnnotationAssertion(rdfs:label "NMRPipe software"@en) +SubClassOf( ) + +# Class: (matNMR software) + +AnnotationAssertion(rdfs:label "matNMR software"@en) +SubClassOf( ) + +# Class: (concentration of chemical compound) + +AnnotationAssertion(rdfs:label "concentration of chemical compound"@en) +SubClassOf( ) + +# Class: (manual phase correction) + +AnnotationAssertion(rdfs:label "manual phase correction"@en) +SubClassOf( ) + +# Class: (automatic phase correction) + +AnnotationAssertion(rdfs:label "automatic phase correction"@en) +SubClassOf( ) + +# Class: (DC offset correction) + +AnnotationAssertion(rdfs:label "DC offset correction"@en) +SubClassOf( ) + +# Class: (Gibbs multiplication) + +AnnotationAssertion(rdfs:label "Gibbs multiplication"@en) +SubClassOf( ) + +# Class: (skyline projection) + +AnnotationAssertion(rdfs:label "skyline projection"@en) +SubClassOf( ) + +# Class: (shifted sine window function) + +AnnotationAssertion(rdfs:label "shifted sine window function"@en) +SubClassOf( ) + +# Class: (sinc window multiplication of FID (1D)) + +AnnotationAssertion(rdfs:label "sinc window multiplication of FID (1D)"@en) +SubClassOf( ) + +# Class: (SEM window function) + +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/36") +AnnotationAssertion(rdfs:label "SEM window function"@en) +SubClassOf( ) + +# Class: (trapezoid window function) + +AnnotationAssertion(rdfs:label "trapezoid window function"@en) +SubClassOf( ) + +# Class: (shifted gaussian window function) + +AnnotationAssertion(rdfs:label "shifted gaussian window function"@en) +SubClassOf( ) + +# Class: (baseline correction using spline function) + +AnnotationAssertion(rdfs:label "baseline correction using spline function"@en) +SubClassOf( ) + +# Class: (heteronuclear single quantum coherence spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear single quantum coherence spectrum"@en) +SubClassOf( ) + +# Class: (Zangger-Sterk pulse sequence) + +AnnotationAssertion(rdfs:label "Zangger-Sterk pulse sequence"@en) +SubClassOf( ) + +# Class: (pure shift 1D Zangger-Sterk pulse sequence) + +AnnotationAssertion(rdfs:label "pure shift 1D Zangger-Sterk pulse sequence"@en) +SubClassOf( ) + +# Class: (oneshot pulse sequence) + +AnnotationAssertion(rdfs:label "oneshot pulse sequence"@en) +SubClassOf( ) + +# Class: (pure shift oneshot pulse sequence) + +AnnotationAssertion(rdfs:label "pure shift oneshot pulse sequence"@en) +SubClassOf( ) + +# Class: (perfect echo watergate pulse sequence) + +AnnotationAssertion(rdfs:label "perfect echo watergate pulse sequence"@en) +SubClassOf( ) + +# Class: (NMR Star 3.1 file format) + +AnnotationAssertion(rdfs:label "NMR Star 3.1 file format"@en) +SubClassOf( ) + +# Class: (NMR Star 2.1 file format) + +AnnotationAssertion(rdfs:label "NMR Star 2.1 file format"@en) +SubClassOf( ) + +# Class: (3D spectrum) + +AnnotationAssertion(rdfs:label "3D spectrum"@en) +SubClassOf( ) + +# Class: (4D spectrum) + +AnnotationAssertion(rdfs:label "4D spectrum"@en) +SubClassOf( ) + +# Class: (NMR spectrum by dimensionality) + +AnnotationAssertion(rdfs:label "NMR spectrum by dimensionality"@en) +SubClassOf( ) + +# Class: (homonuclear chemical shift spectrum) + +AnnotationAssertion(rdfs:label "homonuclear chemical shift spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear chemical shift spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear chemical shift spectrum"@en) +SubClassOf( ) + +# Class: (Bruker instrument model) + +AnnotationAssertion( "NMR:1000122") +AnnotationAssertion(rdfs:label "Bruker instrument model") +SubClassOf( ) + +# Class: (homonuclear exchange spectroscopy spectrum) + +AnnotationAssertion(rdfs:label "homonuclear exchange spectroscopy spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear exchange spectroscopy spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear exchange spectroscopy spectrum"@en) +SubClassOf( ) + +# Class: (homonuclear J-resolved spectrum) + +AnnotationAssertion(rdfs:label "homonuclear J-resolved spectrum"@en) +SubClassOf( ) + +# Class: (heteronuclear J-resolved spectrum) + +AnnotationAssertion(rdfs:label "heteronuclear J-resolved spectrum"@en) +SubClassOf( ) + +# Class: (calibration test spectrum) + +AnnotationAssertion(rdfs:label "calibration test spectrum"@en) +SubClassOf( ) + +# Class: (NMR star software) + +AnnotationAssertion(rdfs:label "NMR star software"@en) +SubClassOf( ) + +# Class: (Felix software) + +AnnotationAssertion(rdfs:label "Felix software"@en) +SubClassOf( ) + +# Class: (PIPP software) + +AnnotationAssertion(rdfs:label "PIPP software"@en) +SubClassOf( ) + +# Class: (TALOS+ software) + +AnnotationAssertion(rdfs:label "TALOS+ software"@en) +SubClassOf( ) + +# Class: (CYANA software) + +AnnotationAssertion(rdfs:label "CYANA software"@en) +SubClassOf( ) + +# Class: (XPLOR-NIH software) + +AnnotationAssertion(rdfs:label "XPLOR-NIH software"@en) +SubClassOf( ) + +# Class: (computed concentration) + +AnnotationAssertion(rdfs:label "computed concentration"@en) +SubClassOf( ) + +# Class: (XEASY software) + +AnnotationAssertion(rdfs:label "XEASY software"@en) +SubClassOf( ) + +# Class: (sparky software) + +AnnotationAssertion(rdfs:label "sparky software"@en) +SubClassOf( ) + +# Class: (CARA software) + +AnnotationAssertion(rdfs:label "CARA software"@en) +SubClassOf( ) + +# Class: (Wattos software) + +AnnotationAssertion(rdfs:label "Wattos software"@en) +SubClassOf( ) + +# Class: (MADNMR software) + +AnnotationAssertion(rdfs:label "MADNMR software"@en) +SubClassOf( ) + +# Class: (Pronto software) + +AnnotationAssertion(rdfs:label "Pronto software"@en) +SubClassOf( ) + +# Class: (TRIAD NMR software) + +AnnotationAssertion(rdfs:label "TRIAD NMR software"@en) +SubClassOf( ) + +# Class: (library based computed concentration) + +AnnotationAssertion(rdfs:label "library based computed concentration"@en) +SubClassOf( ) + +# Class: (Lorenzian estimated concentration) + +AnnotationAssertion(rdfs:label "Lorenzian estimated concentration"@en) +SubClassOf( ) + +# Class: (measured area based concentration) + +AnnotationAssertion(rdfs:label "measured area based concentration"@en) +SubClassOf( ) + +# Class: (time-domain amplitude computed concentration) + +AnnotationAssertion(rdfs:label "time-domain amplitude computed concentration"@en) +SubClassOf( ) + +# Class: (group time delay compensation) + +AnnotationAssertion(rdfs:label "group time delay compensation"@en) +SubClassOf( ) + +# Class: (scaling by forward linear prediction) + +AnnotationAssertion(rdfs:label "scaling by forward linear prediction"@en) +SubClassOf( ) + +# Class: (back calculation of first points by linear-prediction) + +AnnotationAssertion(rdfs:label "back calculation of first points by linear-prediction"@en) +SubClassOf( ) + +# Class: (scaling by mirror image linear prediction) + +AnnotationAssertion(rdfs:label "scaling by mirror image linear prediction"@en) +SubClassOf( ) + +# Class: (digital filtering) + +AnnotationAssertion(rdfs:label "digital filtering"@en) +SubClassOf( ) + +# Class: (3D strip plot generation) + +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion(rdfs:label "3D strip plot generation"@en) +SubClassOf( ) + +# Class: (Batman software) + +AnnotationAssertion(rdfs:label "Batman software"@en) +SubClassOf( ) + +# Class: (JEOL instrument model) + +AnnotationAssertion(rdfs:label "JEOL instrument model"@en) +SubClassOf( ) + +# Class: (tecmag instrument model) + +AnnotationAssertion(rdfs:label "tecmag instrument model"@en) +SubClassOf( ) + +# Class: (automatic baseline recognition) + +AnnotationAssertion(rdfs:label "automatic baseline recognition"@en) +SubClassOf( ) + +# Class: (Trimethylsilyl propionate) + +AnnotationAssertion(rdfs:label "Trimethylsilyl propionate"@en) +SubClassOf( ) + +# Class: (TMIC lab pulse sequence) + +AnnotationAssertion(rdfs:label "TMIC lab pulse sequence"@en) +SubClassOf( ) + +# Class: (probe gradient strength) + +AnnotationAssertion(rdfs:label "probe gradient strength"@en) +SubClassOf( ) + +# Class: (NMR acquisition computer operating system) + +AnnotationAssertion(rdfs:label "NMR acquisition computer operating system"@en) +SubClassOf( ) + +# Class: (NMR autosampler software) + +AnnotationAssertion(rdfs:label "NMR autosampler software"@en) +SubClassOf( ) + +# Class: (Bruker Biospin ICON-NMR software) + +AnnotationAssertion(rdfs:label "Bruker Biospin ICON-NMR software"@en) +SubClassOf( ) + +# Class: (buffer pH) + +AnnotationAssertion(rdfs:label "buffer pH"@en) +SubClassOf( ) + +# Class: (field frequency lock) + +AnnotationAssertion(rdfs:label "field frequency lock"@en) +SubClassOf( ) + +# Class: (concentration standard) + +AnnotationAssertion(rdfs:label "concentration standard"@en) +SubClassOf( ) + +# Class: (NMR acquisition software) + +AnnotationAssertion(rdfs:label "NMR acquisition software"@en) +SubClassOf( ) + +# Class: (CIMR MI standard) + +AnnotationAssertion(rdfs:label "CIMR MI standard"@en) +SubClassOf( ) + +# Class: (signal line width check) + +AnnotationAssertion(rdfs:label "signal line width check"@en) +SubClassOf( ) + +# Class: (signal line width at five percent intensity check) + +AnnotationAssertion(rdfs:label "signal line width at five percent intensity check"@en) +SubClassOf( ) + +# Class: (NMR spectrum descriptor) + +AnnotationAssertion(rdfs:label "NMR spectrum descriptor"@en) +SubClassOf( ) + +# Class: (pulse width) + +AnnotationAssertion(rdfs:label "pulse width"@en) +SubClassOf( ) + +# Class: (hard pulse width) + +AnnotationAssertion(rdfs:label "hard pulse width"@en) +SubClassOf( ) + +# Class: (sweep width) + +AnnotationAssertion(rdfs:label "sweep width"@en) +SubClassOf( ) + +# Class: (number of data points) + +AnnotationAssertion(rdfs:label "number of data points"@en) +SubClassOf( ) + +# Class: (x end value) + +AnnotationAssertion( "tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.") +AnnotationAssertion(rdfs:label "x end value"@en) +SubClassOf( ) + +# Class: (y-axis type) + +AnnotationAssertion(rdfs:label "y-axis type"@en) +SubClassOf( ) + +# Class: (center of bin on x-axis) + +AnnotationAssertion(rdfs:label "center of bin on x-axis"@en) +SubClassOf( ) + +# Class: (spectral quantitation algorithm) + +AnnotationAssertion(rdfs:label "spectral quantitation algorithm"@en) +SubClassOf( ) + +# Class: (NMRProcFlow software) + +AnnotationAssertion( "The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization."@en) +AnnotationAssertion(rdfs:label "NMRProcFlow software"@en) +SubClassOf( ) + +# Class: (Bayesil software) + +AnnotationAssertion( "Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture."@en) +AnnotationAssertion(rdfs:label "Bayesil software"@en) +SubClassOf( ) + +# Class: (nmrML Assign) + +AnnotationAssertion( "nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format."@en) +AnnotationAssertion(rdfs:label "nmrML Assign"@en) +SubClassOf( ) + +# Class: (doublet feature) + +AnnotationAssertion(rdfs:label "doublet feature"@en) +SubClassOf( ) + +# Class: (triplet feature) + +AnnotationAssertion(rdfs:label "triplet feature"@en) +SubClassOf( ) + +# Class: (quatruplet feature) + +AnnotationAssertion(rdfs:label "quatruplet feature"@en) +SubClassOf( ) + +# Class: (cluster of peaks across samples) + +AnnotationAssertion( "a set of peaks that are highly correlated in a series of samples") +AnnotationAssertion(rdfs:label "cluster of peaks across samples"@en) +SubClassOf( ) + +# Class: (simulated spectrum) + +AnnotationAssertion(rdfs:label "simulated spectrum"@en) +SubClassOf( ) + +# Class: (pulse parameter) + +AnnotationAssertion(rdfs:label "pulse parameter"@en) +SubClassOf( ) + +# Class: (JEOL FID format) + +AnnotationAssertion(rdfs:label "JEOL FID format"@en) +SubClassOf( ) + +# Class: (doublet of doublets feature) + +AnnotationAssertion(rdfs:label "doublet of doublets feature"@en) +SubClassOf( ) + +# Class: (ABX multiplet pattern) + +AnnotationAssertion(rdfs:label "ABX multiplet pattern"@en) +SubClassOf( ) + +# Class: (singlet feature) + +AnnotationAssertion(rdfs:label "singlet feature"@en) +SubClassOf( ) + +# Class: (quintet feature) + +AnnotationAssertion(rdfs:label "quintet feature"@en) +SubClassOf( ) + +# Class: (doublet of triplets) + +AnnotationAssertion(rdfs:label "doublet of triplets"@en) +SubClassOf( ) + +# Class: (triplet of douplets) + +AnnotationAssertion(rdfs:label "triplet of douplets"@en) +SubClassOf( ) + +# Class: (triplet of triplets) + +AnnotationAssertion(rdfs:label "triplet of triplets"@en) +SubClassOf( ) + +# Class: (NMR spectrum by pulse sequence) + +AnnotationAssertion(rdfs:label "NMR spectrum by pulse sequence"@en) +SubClassOf( ) + +# Class: (NMR spectrum by processing step) + +AnnotationAssertion(rdfs:label "NMR spectrum by processing step"@en) +SubClassOf( ) + +# Class: (2D spectrum coordinate system descriptor) + +AnnotationAssertion(rdfs:label "2D spectrum coordinate system descriptor"@en) +SubClassOf( ) + +# Class: (y-axis value type) + +AnnotationAssertion(rdfs:label "y-axis value type"@en) +SubClassOf( ) + +# Class: (power value type) + +AnnotationAssertion(rdfs:label "power value type"@en) +SubClassOf( ) + +# Class: (magnitude value type) + +AnnotationAssertion(rdfs:label "magnitude value type"@en) +SubClassOf( ) + +# Class: (real value type) + +AnnotationAssertion(rdfs:label "real value type"@en) +SubClassOf( ) + +# Class: (imaginary value type) + +AnnotationAssertion(rdfs:label "imaginary value type"@en) +SubClassOf( ) + +# Class: (complex value types) + +AnnotationAssertion(rdfs:label "complex value types"@en) +SubClassOf( ) + +# Class: (spectral projection axis) + +AnnotationAssertion(rdfs:label "spectral projection axis"@en) +SubClassOf( ) + +# Class: (f1 axis) + +AnnotationAssertion(rdfs:label "f1 axis"@en) +SubClassOf( ) + +# Class: (f2 axis) + +AnnotationAssertion(rdfs:label "f2 axis"@en) +SubClassOf( ) + +# Class: (NMR Format converter) + +AnnotationAssertion(rdfs:label "NMR Format converter"@en) +SubClassOf( ) + +# Class: (BML-NMR identifier) + +AnnotationAssertion(rdfs:label "BML-NMR identifier"@en) +SubClassOf( ) + +# Class: (creatinine) + +AnnotationAssertion(rdfs:label "creatinine"@en) +SubClassOf( ) + +# Class: (2D pulse sequence) + +AnnotationAssertion(rdfs:label "2D pulse sequence"@en) +SubClassOf( ) + +# Class: (data simulation) + +AnnotationAssertion(rdfs:label "data simulation"@en) +SubClassOf( ) + +# Class: (dynamic nuclear polarization NMR) + +AnnotationAssertion(rdfs:label "dynamic nuclear polarization NMR"@en) +SubClassOf( ) + +# Class: (chemical shift) + +AnnotationAssertion( "Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis") +AnnotationAssertion(rdfs:label "chemical shift"@en) +SubClassOf( ) + +# Class: (nmr signal intensity) + +AnnotationAssertion( "an information object that describes the strength of the NMR signal") +AnnotationAssertion(rdfs:label "nmr signal intensity"@en) +SubClassOf( ) + +# Class: (baseline correction using polynomial function) + +AnnotationAssertion(rdfs:label "baseline correction using polynomial function"@en) +SubClassOf( ) + +# Class: (first transient of the tnnoesy-presaturation pulse sequence) + +AnnotationAssertion(rdfs:label "first transient of the tnnoesy-presaturation pulse sequence"@en) +SubClassOf( ) + +# Class: (Varian acquisition parameter file) + +AnnotationAssertion(rdfs:label "Varian acquisition parameter file"@en) +SubClassOf( ) + +# Class: (procpar) + +AnnotationAssertion(rdfs:label "procpar"@en) +SubClassOf( ) + +# Class: (acqus) + +AnnotationAssertion(rdfs:label "acqus"@en) +SubClassOf( ) + +# Class: (Bruker acquisition parameter file) + +AnnotationAssertion(rdfs:label "Bruker acquisition parameter file"@en) +SubClassOf( ) + +# Class: (peak feature) + +AnnotationAssertion( "NMR:1000231") +AnnotationAssertion(rdfs:label "peak feature") +SubClassOf( ) + +# Class: (global) + +AnnotationAssertion(rdfs:label "global"@en) +SubClassOf( ) + +# Class: (Varian autosampler) + +AnnotationAssertion(rdfs:label "Varian autosampler"@en) +SubClassOf( ) + +# Class: (Varian SMS 50) + +AnnotationAssertion(rdfs:label "Varian SMS 50"@en) +SubClassOf( ) + +# Class: (Varian probe) + +AnnotationAssertion(rdfs:label "Varian probe"@en) +SubClassOf( ) + +# Class: (5mm HCN probe) + +AnnotationAssertion(rdfs:label "5mm HCN probe"@en) +SubClassOf( ) + +# Class: (Varian liquid cold probe) + +AnnotationAssertion(rdfs:label "Varian liquid cold probe"@en) +SubClassOf( ) + +# Class: (reference compound NMR spectrum) + +AnnotationAssertion(rdfs:label "reference compound NMR spectrum"@en) +SubClassOf( ) + +# Class: (Mestrelab software) + +AnnotationAssertion(rdfs:label "Mestrelab software"@en) +SubClassOf( ) + +# Class: (ACD spectrus software) + +AnnotationAssertion(rdfs:label "ACD spectrus software"@en) +SubClassOf( ) + +# Class: (Mat NMR 3 software) + +AnnotationAssertion(rdfs:label "Mat NMR 3 software"@en) +SubClassOf( ) + +# Class: (NMRLab software) + +AnnotationAssertion(rdfs:label "NMRLab software"@en) +SubClassOf( ) + +# Class: (Spinworks NMR software) + +AnnotationAssertion(rdfs:label "Spinworks NMR software"@en) +SubClassOf( ) + +# Class: (NMR software vendor) + +AnnotationAssertion(rdfs:label "NMR software vendor"@en) +SubClassOf( ) + +# Class: (Spinworks) + +AnnotationAssertion(rdfs:label "Spinworks"@en) +SubClassOf( ) + +# Class: (iNMR software) + +AnnotationAssertion(rdfs:label "iNMR software"@en) +SubClassOf( ) + +# Class: (NMR pipe) + +AnnotationAssertion(rdfs:label "NMR pipe"@en) +SubClassOf( ) + +# Class: (cule NMR software) + +AnnotationAssertion(rdfs:label "cule NMR software"@en) +SubClassOf( ) + +# Class: (Matlab to nmrML converter) + +AnnotationAssertion(rdfs:label "Matlab to nmrML converter"@en) +SubClassOf( ) + +# Class: (Bruker processing parameter file) + +AnnotationAssertion(rdfs:label "Bruker processing parameter file"@en) +SubClassOf( ) + +# Class: (procs) + +AnnotationAssertion(rdfs:label "procs"@en) +SubClassOf( ) + +# Class: (Varian processing parameter file) + +AnnotationAssertion(rdfs:label "Varian processing parameter file"@en) +SubClassOf( ) + +# Class: (Madison Metabolomics Consortium Database MMCD identifier) + +AnnotationAssertion(rdfs:label "Madison Metabolomics Consortium Database MMCD identifier"@en) +SubClassOf( ) + +# Class: (Bigg metabolomics database identifier) + +AnnotationAssertion(rdfs:label "Bigg metabolomics database identifier"@en) +SubClassOf( ) + +# Class: (Lorentz Gaussian window function) + +AnnotationAssertion(rdfs:label "Lorentz Gaussian window function"@en) +SubClassOf( ) + +# Class: (traf window function) + +AnnotationAssertion(rdfs:label "traf window function"@en) +SubClassOf( ) + +# Class: (trafs window function) + +AnnotationAssertion(rdfs:label "trafs window function"@en) +SubClassOf( ) + +# Class: (peak fitting) + +AnnotationAssertion(rdfs:label "peak fitting"@en) +SubClassOf( ) + +# Class: (peak assignment) + +AnnotationAssertion(rdfs:label "peak assignment"@en) +SubClassOf( ) + +# Class: (deconvolution) + +AnnotationAssertion(rdfs:label "deconvolution"@en) +SubClassOf( ) + +# Class: (chemical shift sorting) + +AnnotationAssertion( "A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks.") +AnnotationAssertion(rdfs:label "chemical shift sorting"@en) +SubClassOf( ) + +# Class: (fid file) + +AnnotationAssertion(rdfs:label "fid file"@en) +SubClassOf( ) + +# Class: (Varian FID file) + +AnnotationAssertion(rdfs:label "Varian FID file"@en) +SubClassOf( ) + +# Class: (Bruker FID file) + +AnnotationAssertion(rdfs:label "Bruker FID file"@en) +SubClassOf( ) + +# Class: (ERVA-based bucketing) + +AnnotationAssertion(rdfs:label "ERVA-based bucketing"@en) +SubClassOf( ) + +# Class: (cluster of peaks) + +AnnotationAssertion(rdfs:label "cluster of peaks"@en) +SubClassOf( ) + +# Class: (Match NMR tube) + +AnnotationAssertion(rdfs:label "Match NMR tube"@en) +SubClassOf( ) + +# Class: (shaped tube) + +AnnotationAssertion(rdfs:label "shaped tube"@en) +SubClassOf( ) + +# Class: (Shigemi tube) + +AnnotationAssertion(rdfs:label "Shigemi tube"@en) +SubClassOf( ) + +# Class: (standard tube) + +AnnotationAssertion(rdfs:label "standard tube"@en) +SubClassOf( ) + +# Class: (Bruker tube) + +AnnotationAssertion(rdfs:label "Bruker tube"@en) +SubClassOf( ) + +# Class: (JEOL magnet) + +AnnotationAssertion(rdfs:label "JEOL magnet"@en) +SubClassOf( ) + +# Class: (JEOL ECS magnet) + +AnnotationAssertion(rdfs:label "JEOL ECS magnet"@en) +SubClassOf( ) + +# Class: (JEOL ECA magnet) + +AnnotationAssertion(rdfs:label "JEOL ECA magnet"@en) +SubClassOf( ) + +# Class: (JEOL ECX magnet) + +AnnotationAssertion(rdfs:label "JEOL ECX magnet"@en) +SubClassOf( ) + +# Class: (Varian NMR software) + +AnnotationAssertion(rdfs:label "Varian NMR software"@en) +SubClassOf( ) + +# Class: (VnmrJ software) + +AnnotationAssertion(rdfs:label "VnmrJ software"@en) +SubClassOf( ) + +# Class: (Wilmad tube) + +AnnotationAssertion(rdfs:label "Wilmad tube"@en) +SubClassOf( ) + +# Class: (4mm Match tube) + +AnnotationAssertion(rdfs:label "4mm Match tube"@en) +SubClassOf( ) + +# Class: (2.5mm Match tube) + +AnnotationAssertion(rdfs:label "2.5mm Match tube"@en) +SubClassOf( ) + +# Class: (3mm Match tube) + +AnnotationAssertion(rdfs:label "3mm Match tube"@en) +SubClassOf( ) + +# Class: (5mm Match tube) + +AnnotationAssertion(rdfs:label "5mm Match tube"@en) +SubClassOf( ) + +# Class: (1mm Match tube) + +AnnotationAssertion(rdfs:label "1mm Match tube"@en) +SubClassOf( ) + +# Class: (1.7mm Match tube) + +AnnotationAssertion(rdfs:label "1.7mm Match tube"@en) +SubClassOf( ) + +# Class: (2mm Match tube) + +AnnotationAssertion(rdfs:label "2mm Match tube"@en) +SubClassOf( ) + +# Class: (4.25mm Match tube) + +AnnotationAssertion(rdfs:label "4.25mm Match tube"@en) +SubClassOf( ) + +# Class: (3mm standard tube) + +AnnotationAssertion(rdfs:label "3mm standard tube"@en) +SubClassOf( ) + +# Class: (5mm standard tube) + +AnnotationAssertion(rdfs:label "5mm standard tube"@en) +SubClassOf( ) + +# Class: (1mm standard tube) + +AnnotationAssertion(rdfs:label "1mm standard tube"@en) +SubClassOf( ) + +# Class: (1.7mm standard tube) + +AnnotationAssertion(rdfs:label "1.7mm standard tube"@en) +SubClassOf( ) + +# Class: (Wilmad economy tube) + +AnnotationAssertion(rdfs:label "Wilmad economy tube"@en) +SubClassOf( ) + +# Class: (Wilmad precision tube) + +AnnotationAssertion(rdfs:label "Wilmad precision tube"@en) +SubClassOf( ) + +# Class: (Norell tube) + +AnnotationAssertion(rdfs:label "Norell tube"@en) +SubClassOf( ) + +# Class: (JEOL FID file) + +AnnotationAssertion(rdfs:label "JEOL FID file"@en) +SubClassOf( ) + +# Class: (nmRIO) + +AnnotationAssertion(rdfs:label "nmRIO"@en) +SubClassOf( ) + +# Class: (rNMR-IO) + +AnnotationAssertion(rdfs:label "rNMR-IO"@en) +SubClassOf( ) + +# Class: (Vendor2nmrML_Java) + +AnnotationAssertion( "Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. +As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. + +The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. + +The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step."@en) +AnnotationAssertion(rdfs:label "Vendor2nmrML_Java"@en) +SubClassOf( ) + +# Class: (Varian magnet) + +AnnotationAssertion(rdfs:label "Varian magnet"@en) +SubClassOf( ) + +# Class: (premium compact narrow bore magnet) + +AnnotationAssertion(rdfs:label "premium compact narrow bore magnet"@en) +SubClassOf( ) + +# Class: (premium shielded narrow bore magnet) + +AnnotationAssertion(rdfs:label "premium shielded narrow bore magnet"@en) +SubClassOf( ) + +# Class: (premium shielded wide bore magnet) + +AnnotationAssertion(rdfs:label "premium shielded wide bore magnet"@en) +SubClassOf( ) + +# Class: (modified Gaussian window function) + +AnnotationAssertion(rdfs:label "modified Gaussian window function"@en) +SubClassOf( ) + +# Class: (exponentially damped J-modulation window function) + +AnnotationAssertion(rdfs:label "exponentially damped J-modulation window function"@en) +SubClassOf( ) + +# Class: (shifted sine bell window function) + +AnnotationAssertion(rdfs:label "shifted sine bell window function"@en) +SubClassOf( ) + +# Class: (triangle window function) + +AnnotationAssertion(rdfs:label "triangle window function"@en) +SubClassOf( ) + +# Class: (acquisition log file) + +AnnotationAssertion( "The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.") +AnnotationAssertion(rdfs:label "acquisition log file"@en) +SubClassOf( ) + +# Class: (PynmrML) + +AnnotationAssertion(rdfs:label "PynmrML"@en) +SubClassOf( ) + +# Class: (MetaboAnalyst software) + +AnnotationAssertion( "A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources."@en) +AnnotationAssertion(rdfs:label "MetaboAnalyst software"@en) +SubClassOf( ) + +# Class: (acqu2s) + +AnnotationAssertion(rdfs:label "acqu2s"@en) +SubClassOf( ) + +# Class: (acqu3s) + +AnnotationAssertion(rdfs:label "acqu3s"@en) +SubClassOf( ) + +# Class: (proc2s) + +AnnotationAssertion(rdfs:label "proc2s"@en) +SubClassOf( ) + +# Class: (proc3s) + +AnnotationAssertion(rdfs:label "proc3s"@en) +SubClassOf( ) + +# Class: (NMR spectrum file) + +AnnotationAssertion(rdfs:label "NMR spectrum file"@en) +SubClassOf( ) + +# Class: (Bruker NMR spectrum file) + +AnnotationAssertion(rdfs:label "Bruker NMR spectrum file"@en) +SubClassOf( ) + +# Class: (1R file) + +AnnotationAssertion(rdfs:label "1R file"@en) +SubClassOf( ) + +# Class: (title file) + +AnnotationAssertion(rdfs:label "title file"@en) +SubClassOf( ) + +# Class: (XEASY software) + +AnnotationAssertion( "A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes."@en) +AnnotationAssertion(rdfs:label "XEASY software"@en) +SubClassOf( ) + +# Class: (NMR spectrum vizualisation software) + +AnnotationAssertion(rdfs:label "NMR spectrum vizualisation software"@en) +SubClassOf( ) + +# Class: (JspectraView software) + +AnnotationAssertion(rdfs:label "JspectraView software"@en) +SubClassOf( ) + +# Class: (cryoprobe) + +AnnotationAssertion(rdfs:label "cryoprobe"@en) +SubClassOf( ) + +# Class: (inverse detection NMR probe) + +AnnotationAssertion(rdfs:label "inverse detection NMR probe"@en) +SubClassOf( ) + +# Class: (5mm inverse detection cryoprobe) + +AnnotationAssertion(rdfs:label "5mm inverse detection cryoprobe"@en) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (NMRViewer software) + +AnnotationAssertion(rdfs:label "NMRViewer software"@en) +SubClassOf( ) + +# Class: (AB multiplet pattern) + +AnnotationAssertion(rdfs:label "AB multiplet pattern"@en) +SubClassOf( ) + +# Class: (NMR solvent) + +AnnotationAssertion(rdfs:label "NMR solvent"@en) +SubClassOf( ) + +# Class: (NMR buffer) + +AnnotationAssertion(rdfs:label "NMR buffer"@en) +SubClassOf( ) + +# Class: (presat water suppression) + +AnnotationAssertion(rdfs:label "presat water suppression"@en) +SubClassOf( ) + +# Class: (Varian VNMRS 600) + +AnnotationAssertion(rdfs:label "Varian VNMRS 600"@en) +SubClassOf( ) + +# Class: (data content encoding) + +AnnotationAssertion(rdfs:label "data content encoding"@en) +SubClassOf( ) + +# Class: (data compression scheme) + +AnnotationAssertion(rdfs:label "data compression scheme"@en) +SubClassOf( ) + +# Class: (byte format) + +AnnotationAssertion(rdfs:label "byte format"@en) +SubClassOf( ) + +# Class: (zlib) + +AnnotationAssertion(rdfs:label "zlib"@en) +SubClassOf( ) + +# Class: (complex64) + +AnnotationAssertion(rdfs:label "complex64"@en) +SubClassOf( ) + +# Class: (complex128) + +AnnotationAssertion(rdfs:label "complex128"@en) +SubClassOf( ) + +# Class: (binary data compression type) + +AnnotationAssertion(rdfs:label "binary data compression type"@en) +SubClassOf( ) + +# Class: (AB2 multiplet pattern) + +AnnotationAssertion(rdfs:label "AB2 multiplet pattern"@en) +SubClassOf( ) + +# Class: (data encoding parameter) + +AnnotationAssertion(rdfs:label "data encoding parameter"@en) +SubClassOf( ) + +# Class: (uncompressed data) + +AnnotationAssertion(rdfs:label "uncompressed data"@en) +SubClassOf( ) + +# Class: (digital signal processing firmware version) + +AnnotationAssertion( "DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer") +AnnotationAssertion(rdfs:label "digital signal processing firmware version"@en) +SubClassOf( ) + +# Class: (decimation factor) + +AnnotationAssertion( "DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid.") +AnnotationAssertion(rdfs:label "decimation factor"@en) +SubClassOf( ) + +# Class: (group time delay) + +AnnotationAssertion( "GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. \"The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.\")") +AnnotationAssertion(rdfs:label "group time delay"@en) +SubClassOf( ) + +# Class: (NMR sampling strategy) + +AnnotationAssertion(rdfs:label "NMR sampling strategy"@en) +SubClassOf( ) + +# Class: (uniform sampling) + +AnnotationAssertion(rdfs:label "uniform sampling"@en) +SubClassOf( ) + +# Class: (non-uniform sampling) + +AnnotationAssertion(rdfs:label "non-uniform sampling"@en) +SubClassOf( ) + +# Class: (Bruker XWIN-NMR software) + +AnnotationAssertion(rdfs:label "Bruker XWIN-NMR software"@en) +SubClassOf( ) + +# Class: (software attribute) + +AnnotationAssertion(rdfs:label "software attribute"@en) +SubClassOf( ) + +# Class: (NMR software version) + +AnnotationAssertion(rdfs:label "NMR software version"@en) +SubClassOf( ) + +# Class: (ABX3 multiplet pattern) + +AnnotationAssertion(rdfs:label "ABX3 multiplet pattern"@en) +SubClassOf( ) + +# Class: (AA'BB' multiplet pattern) + +AnnotationAssertion(rdfs:label "AA'BB' multiplet pattern"@en) +SubClassOf( ) + +# Class: (AA'XX' multiplet pattern) + +AnnotationAssertion(rdfs:label "AA'XX' multiplet pattern"@en) +SubClassOf( ) + +# Class: (variable size bucketing) + +AnnotationAssertion(rdfs:label "variable size bucketing"@en) +SubClassOf( ) + +# Class: (uniform bucketing) + +AnnotationAssertion(rdfs:label "uniform bucketing"@en) +SubClassOf( ) + +# Class: (intelligent bucketing) + +AnnotationAssertion(rdfs:label "intelligent bucketing"@en) +SubClassOf( ) + +# Class: (bucket importing) + +AnnotationAssertion(rdfs:label "bucket importing"@en) +SubClassOf( ) + +# Class: (bucket resetting) + +AnnotationAssertion(rdfs:label "bucket resetting"@en) +SubClassOf( ) + +# Class: (global baseline correction) + +AnnotationAssertion(rdfs:label "global baseline correction"@en) +SubClassOf( ) + +# Class: (local baseline correction) + +AnnotationAssertion(rdfs:label "local baseline correction"@en) +SubClassOf( ) + +# Class: (bucket fusioning) + +AnnotationAssertion(rdfs:label "bucket fusioning"@en) +SubClassOf( ) + +# Class: (JNM-ECX Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECX Series FT NMR instrument"@en) +SubClassOf( ) + +# Class: (JNM-ECZR Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECZR Series FT NMR instrument"@en) +SubClassOf( ) + +# Class: (JNM-ECZS Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECZS Series FT NMR instrument"@en) +SubClassOf( ) + +# Class: (AVANCE III HD) + +AnnotationAssertion(rdfs:label "AVANCE III HD"@en) +SubClassOf( ) + +# Class: (NanoBay400 MHz) + +AnnotationAssertion(rdfs:label "NanoBay400 MHz"@en) +SubClassOf( ) + +# Class: (Fourier 300HD) + +AnnotationAssertion(rdfs:label "Fourier 300HD"@en) +SubClassOf( ) + +# Class: (DNP-NMR) + +AnnotationAssertion(rdfs:label "DNP-NMR"@en) +SubClassOf( ) + +# Class: (LC-NMR instrument) + +AnnotationAssertion(rdfs:label "LC-NMR instrument"@en) +SubClassOf( ) + +# Class: (LC-NMR/MS instrument) + +AnnotationAssertion(rdfs:label "LC-NMR/MS instrument"@en) +SubClassOf( ) + +# Class: (Food-Screener instrument) + +AnnotationAssertion(rdfs:label "Food-Screener instrument"@en) +SubClassOf( ) + +# Class: (AVANCE IVDr) + +AnnotationAssertion(rdfs:label "AVANCE IVDr"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 400MHz YH magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 400MHz YH magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 500MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 500MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 600MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 600MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 700MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 700MHz magnet"@en) +SubClassOf( ) + +# Class: (JEOL Resonance 800MHz magnet) + +AnnotationAssertion(rdfs:label "JEOL Resonance 800MHz magnet"@en) +SubClassOf( ) + +# Class: (single peak feature) + +AnnotationAssertion(rdfs:label "single peak feature"@en) +SubClassOf( ) + +# Class: (NMR instrument vendor) + +AnnotationAssertion(rdfs:label "NMR instrument vendor"@en) +SubClassOf( ) + +# Class: (Avance I spectrometer) + +AnnotationAssertion(rdfs:label "Avance I spectrometer"@en) +SubClassOf( ) + +# Class: (Oxford Instruments) + +AnnotationAssertion(rdfs:label "Oxford Instruments"@en) +SubClassOf( ) + +# Class: (Spinlock SRL) + +AnnotationAssertion(rdfs:label "Spinlock SRL"@en) +SubClassOf( ) + +# Class: (General Electric) + +AnnotationAssertion(rdfs:label "General Electric"@en) +SubClassOf( ) + +# Class: (Kimble Chase) + +AnnotationAssertion(rdfs:label "Kimble Chase"@en) +SubClassOf( ) + +# Class: (Phillips) + +AnnotationAssertion(rdfs:label "Phillips"@en) +SubClassOf( ) + +# Class: (Siemens AG) + +AnnotationAssertion(rdfs:label "Siemens AG"@en) +SubClassOf( ) + +# Class: (Varian Inova 500) + +AnnotationAssertion(rdfs:label "Varian Inova 500"@en) +SubClassOf( ) + +# Class: (Varian VNMRS instrument) + +AnnotationAssertion(rdfs:label "Varian VNMRS instrument"@en) +SubClassOf( ) + +# Class: (Varian Mercury plus) + +AnnotationAssertion(rdfs:label "Varian Mercury plus"@en) +SubClassOf( ) + +# Class: (Varian UnityInova instrument) + +AnnotationAssertion(rdfs:label "Varian UnityInova instrument"@en) +SubClassOf( ) + +# Class: (Varian 400-MR NMR instrument) + +AnnotationAssertion(rdfs:label "Varian 400-MR NMR instrument"@en) +SubClassOf( ) + +# Class: (Varian DDR2 instrument) + +AnnotationAssertion(rdfs:label "Varian DDR2 instrument"@en) +SubClassOf( ) + +# Class: (Agilent NMR instrument) + +AnnotationAssertion(rdfs:label "Agilent NMR instrument"@en) +SubClassOf( ) + +# Class: (Agilent 400-MR NMR instrument) + +AnnotationAssertion(rdfs:label "Agilent 400-MR NMR instrument"@en) +SubClassOf( ) + +# Class: (Varian Mercury 400) + +AnnotationAssertion(rdfs:label "Varian Mercury 400"@en) +SubClassOf( ) + +# Class: (Agilent Au 400 (DDR2 Console)) + +AnnotationAssertion(rdfs:label "Agilent Au 400 (DDR2 Console)"@en) +SubClassOf( ) + +# Class: (Agilent DDR 2 w/ HCN cryoprobe) + +AnnotationAssertion(rdfs:label "Agilent DDR 2 w/ HCN cryoprobe"@en) +SubClassOf( ) + +# Class: (BMRB identifier) + +AnnotationAssertion(rdfs:label "BMRB identifier"@en) +SubClassOf( ) + +# Class: (left trapezoid limit) + +AnnotationAssertion(rdfs:label "left trapezoid limit"@en) +SubClassOf( ) + +# Class: (trapezoid window function parameter) + +AnnotationAssertion(rdfs:label "trapezoid window function parameter"@en) +SubClassOf( ) + +# Class: (complex64 Integer) + +AnnotationAssertion(rdfs:label "complex64 Integer"@en) +SubClassOf( ) + +# Class: (complex128 Integer) + +AnnotationAssertion(rdfs:label "complex128 Integer"@en) +SubClassOf( ) + +# Class: (right trapezoid limit) + +AnnotationAssertion(rdfs:label "right trapezoid limit"@en) +SubClassOf( ) + +# Class: (thirty degree pulse duration) + +AnnotationAssertion(rdfs:label "thirty degree pulse duration"@en) +SubClassOf( ) + +# Class: (InChi) + +AnnotationAssertion(rdfs:label "InChi"@en) +SubClassOf( ) + +# Class: (inchikey) + +AnnotationAssertion(rdfs:label "inchikey"@en) +SubClassOf( ) + +# Class: (Wiswesser Line Notation) + +AnnotationAssertion(rdfs:label "Wiswesser Line Notation"@en) +SubClassOf( ) + +# Class: (ROSDAL) + +AnnotationAssertion(rdfs:label "ROSDAL"@en) +SubClassOf( ) + +# Class: (SLN-Tripos) + +AnnotationAssertion(rdfs:label "SLN-Tripos"@en) +SubClassOf( ) + +# Class: (smarts) + +AnnotationAssertion(rdfs:label "smarts"@en) +SubClassOf( ) + +# Class: (line representation) + +AnnotationAssertion(rdfs:label "line representation"@en) +SubClassOf( ) + +# Class: (2D topological molecule representation) + +AnnotationAssertion(rdfs:label "2D topological molecule representation"@en) +SubClassOf( ) + +# Class: (2D bond line structure) + +AnnotationAssertion(rdfs:label "2D bond line structure"@en) +SubClassOf( ) + +# Class: (3D geometrical molecule representation) + +AnnotationAssertion(rdfs:label "3D geometrical molecule representation"@en) +SubClassOf( ) + +# Class: (3D bond line structure) + +AnnotationAssertion(rdfs:label "3D bond line structure"@en) +SubClassOf( ) + +# Class: (CAS number) + +AnnotationAssertion(rdfs:label "CAS number"@en) +SubClassOf( ) + +# Class: (fingerprint model) + +AnnotationAssertion(rdfs:label "fingerprint model"@en) +SubClassOf( ) + +# Class: (molfile) + +AnnotationAssertion(rdfs:label "molfile"@en) +SubClassOf( ) + +# Class: (compound similarity measure) + +AnnotationAssertion(rdfs:label "compound similarity measure"@en) +SubClassOf( ) + +# Class: (Tanimoto similarity) + +AnnotationAssertion(rdfs:label "Tanimoto similarity"@en) +SubClassOf( ) + +# Class: (Gaussian window function parameter) + +AnnotationAssertion(rdfs:label "Gaussian window function parameter"@en) +SubClassOf( ) + +# Class: ( 2,2-Dimethyl-2-silapentane-5-sulfonate) + +AnnotationAssertion(rdfs:label " 2,2-Dimethyl-2-silapentane-5-sulfonate"@en) +SubClassOf( ) + +# Class: (Gaussian maximum position) + +AnnotationAssertion(rdfs:label "Gaussian maximum position"@en) +SubClassOf( ) + +# Class: (2H spectrum reference compound) + +AnnotationAssertion(rdfs:label "2H spectrum reference compound"@en) +SubClassOf( ) + +# Class: (ABX2 multiplet pattern) + +AnnotationAssertion(rdfs:label "ABX2 multiplet pattern"@en) +SubClassOf( ) + +# Class: (DRX 600 instrument) + +AnnotationAssertion(rdfs:label "DRX 600 instrument"@en) +SubClassOf( ) + +# Class: (plot and graph generation) + +AnnotationAssertion(rdfs:label "plot and graph generation"@en) +SubClassOf( ) + +# Class: (reference deconvolution) + +AnnotationAssertion(rdfs:label "reference deconvolution"@en) +SubClassOf( ) + +# Class: (spectral smoothing) + +AnnotationAssertion(rdfs:label "spectral smoothing"@en) +SubClassOf( ) + +# Class: (NMR database format) + +AnnotationAssertion(rdfs:label "NMR database format"@en) +SubClassOf( ) + +# Class: (BMRB/XML file format) + +AnnotationAssertion(rdfs:label "BMRB/XML file format"@en) +SubClassOf( ) + +# Class: (nD spectrum) + +AnnotationAssertion(rdfs:label "nD spectrum"@en) +SubClassOf( ) + +# Class: (NMR data conversion) + +AnnotationAssertion( "NMR:1000452") +AnnotationAssertion(rdfs:label "NMR data conversion") +SubClassOf( ) + +# Class: (sample) + +AnnotationAssertion( "NMR:1000457") +AnnotationAssertion(rdfs:label "sample") +SubClassOf( ) + +# Class: (instrument) + +AnnotationAssertion( "NMR:1000463") +AnnotationAssertion(rdfs:label "instrument") +SubClassOf( ) + +# Class: (Varian/Agilent instrument model) + +AnnotationAssertion( "NMR:1000489") +AnnotationAssertion(rdfs:label "Varian/Agilent instrument model") +SubClassOf( ) + +# Class: (instrument attribute) + +AnnotationAssertion( "NMR:1000496") +AnnotationAssertion(rdfs:label "instrument attribute") +SubClassOf( ) + +# Class: (data file content) + +AnnotationAssertion( "NMR:1000524") +AnnotationAssertion(rdfs:label "data file content") +SubClassOf( ) + +# Class: (instrument serial number) + +AnnotationAssertion( "NMR:1000529") +AnnotationAssertion(rdfs:label "instrument serial number") +SubClassOf( ) + +# Class: (file format conversion) + +AnnotationAssertion( "NMR:1000530") +AnnotationAssertion(rdfs:label "file format conversion") +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion( "NMR:1000531") +AnnotationAssertion(rdfs:label "software") +SubClassOf( ) + +# Class: (object attribute) + +AnnotationAssertion( "NMR:1000547") +AnnotationAssertion(rdfs:label "object attribute") +SubClassOf( ) + +# Class: (sample attribute) + +AnnotationAssertion( "NMR:1000548") +AnnotationAssertion(rdfs:label "sample attribute") +SubClassOf( ) + +# Class: (data file checksum type) + +AnnotationAssertion( "NMR:1000561") +AnnotationAssertion(rdfs:label "data file checksum type") +SubClassOf( ) + +# Class: (MD5) + +AnnotationAssertion( "NMR:1000568") +AnnotationAssertion(rdfs:label "MD5") +SubClassOf( ) + +# Class: (SHA-1) + +AnnotationAssertion( "NMR:1000569") +AnnotationAssertion(rdfs:label "SHA-1") +SubClassOf( ) + +# Class: (NMR raw data file format) + +AnnotationAssertion( "NMR:1000577") +AnnotationAssertion(rdfs:label "NMR raw data file format") +SubClassOf( ) + +# Class: (contact attribute) + +AnnotationAssertion( "NMR:1000585") +AnnotationAssertion(rdfs:label "contact attribute") +SubClassOf( ) + +# Class: (contact name) + +AnnotationAssertion( "NMR:1000586") +AnnotationAssertion(rdfs:label "contact name") +SubClassOf( ) + +# Class: (contact address) + +AnnotationAssertion( "NMR:1000587") +AnnotationAssertion(rdfs:label "contact address") +SubClassOf( ) + +# Class: (contact URL) + +AnnotationAssertion( "NMR:1000588") +AnnotationAssertion(rdfs:label "contact URL") +SubClassOf( ) + +# Class: (contact email) + +AnnotationAssertion( "NMR:1000589") +AnnotationAssertion(rdfs:label "contact email") +SubClassOf( ) + +# Class: (contact organization) + +AnnotationAssertion( "NMR:1000590") +AnnotationAssertion(rdfs:label "contact organization") +SubClassOf( ) + +# Class: (data processing parameter) + +AnnotationAssertion( "NMR:1000630") +AnnotationAssertion(rdfs:label "data processing parameter") +SubClassOf( ) + +# Class: (data processing completion time) + +AnnotationAssertion( "NMR:1000747") +AnnotationAssertion(rdfs:label "data processing completion time") +SubClassOf( ) + +# Class: (FID format) + +AnnotationAssertion( "NMR:1000767") +AnnotationAssertion(rdfs:label "FID format") +SubClassOf( ) + +# Class: (Bruker FID format) + +AnnotationAssertion( "NMR:1000773") +AnnotationAssertion(rdfs:label "Bruker FID format") +SubClassOf( ) + +# Class: (custom unreleased software) + +AnnotationAssertion( "NMR:1000799") +AnnotationAssertion(rdfs:label "custom unreleased software") +SubClassOf( ) + +# Class: (sample preparation information) + +AnnotationAssertion( "NMR:1000831") +AnnotationAssertion(rdfs:label "sample preparation information") +SubClassOf( ) + +# Class: (molecule) + +AnnotationAssertion( "NMR:1000859") +AnnotationAssertion(rdfs:label "molecule") +SubClassOf( ) + +# Class: (peptide) + +AnnotationAssertion( "NMR:1000860") +AnnotationAssertion(rdfs:label "peptide") +SubClassOf( ) + +# Class: (chemical compound attribute) + +AnnotationAssertion( "NMR:1000861") +AnnotationAssertion(rdfs:label "chemical compound attribute") +SubClassOf( ) + +# Class: (isoelectric point) + +AnnotationAssertion( "NMR:1000862") +AnnotationAssertion(rdfs:label "isoelectric point") +SubClassOf( ) + +# Class: (predicted isoelectric point) + +AnnotationAssertion( "NMR:1000863") +AnnotationAssertion(rdfs:label "predicted isoelectric point") +SubClassOf( ) + +# Class: (chemical compound formula) + +AnnotationAssertion( "NMR:1000864") +AnnotationAssertion(rdfs:label "chemical compound formula") +SubClassOf( ) + +# Class: (empirical formula) + +AnnotationAssertion( "NMR:1000865") +AnnotationAssertion(rdfs:label "empirical formula") +SubClassOf( ) + +# Class: (molecular formula) + +AnnotationAssertion( "NMR:1000866") +AnnotationAssertion(rdfs:label "molecular formula") +SubClassOf( ) + +# Class: (structural formula) + +AnnotationAssertion( "NMR:1000867") +AnnotationAssertion(rdfs:label "structural formula") +SubClassOf( ) + +# Class: (SMILES string) + +AnnotationAssertion( "NMR:1000868") +AnnotationAssertion(rdfs:label "SMILES string") +SubClassOf( ) + +# Class: (external reference identifier) + +AnnotationAssertion( "NMR:1000878") +AnnotationAssertion(rdfs:label "external reference identifier") +SubClassOf( ) + +# Class: (PubMed identifier) + +AnnotationAssertion( "NMR:1000879") +AnnotationAssertion(rdfs:label "PubMed identifier") +SubClassOf( ) + +# Class: (chemical compound) + +AnnotationAssertion( "NMR:1000881") +AnnotationAssertion(rdfs:label "chemical compound") +SubClassOf( ) + +# Class: (protein) + +AnnotationAssertion( "NMR:1000882") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) + +# Class: (protein short name) + +AnnotationAssertion( "NMR:1000883") +AnnotationAssertion(rdfs:label "protein short name") +SubClassOf( ) + +# Class: (protein attribute) + +AnnotationAssertion( "NMR:1000884") +AnnotationAssertion(rdfs:label "protein attribute") +SubClassOf( ) + +# Class: (protein accession) + +AnnotationAssertion( "NMR:1000885") +AnnotationAssertion(rdfs:label "protein accession") +SubClassOf( ) + +# Class: (protein name) + +AnnotationAssertion( "NMR:1000886") +AnnotationAssertion(rdfs:label "protein name") +SubClassOf( ) + +# Class: (peptide attribute) + +AnnotationAssertion( "NMR:1000887") +AnnotationAssertion(rdfs:label "peptide attribute") +SubClassOf( ) + +# Class: (unmodified peptide sequence) + +AnnotationAssertion( "NMR:1000888") +AnnotationAssertion(rdfs:label "unmodified peptide sequence") +SubClassOf( ) + +# Class: (modified peptide sequence) + +AnnotationAssertion( "NMR:1000889") +AnnotationAssertion(rdfs:label "modified peptide sequence") +SubClassOf( ) + +# Class: (peptide labeling state) + +AnnotationAssertion( "NMR:1000890") +AnnotationAssertion(rdfs:label "peptide labeling state") +SubClassOf( ) + +# Class: (heavy labeled peptide) + +AnnotationAssertion( "NMR:1000891") +AnnotationAssertion(rdfs:label "heavy labeled peptide") +SubClassOf( ) + +# Class: (unlabeled peptide) + +AnnotationAssertion( "NMR:1000892") +AnnotationAssertion(rdfs:label "unlabeled peptide") +SubClassOf( ) + +# Class: (peptide group label) + +AnnotationAssertion( "NMR:1000893") +AnnotationAssertion(rdfs:label "peptide group label") +SubClassOf( ) + +# Class: (data standard) + +AnnotationAssertion( "NMR:1000898") +AnnotationAssertion(rdfs:label "data standard") +SubClassOf( ) + +# Class: (de facto standard) + +AnnotationAssertion( "NMR:1000899") +AnnotationAssertion(rdfs:label "de facto standard") +SubClassOf( ) + +# Class: (minimum information standard) + +AnnotationAssertion( "NMR:1000900") +AnnotationAssertion(rdfs:label "minimum information standard") +SubClassOf( ) + +# Class: (tab delimited text file) + +AnnotationAssertion( "NMR:1000914") +AnnotationAssertion(rdfs:label "tab delimited text file") +SubClassOf( ) + +# Class: (protein modification) + +AnnotationAssertion( "NMR:1000933") +AnnotationAssertion(rdfs:label "protein modification") +SubClassOf( ) + +# Class: (gene name) + +AnnotationAssertion( "NMR:1000934") +AnnotationAssertion(rdfs:label "gene name") +SubClassOf( ) + +# Class: (intermediate analysis format) + +AnnotationAssertion( "NMR:1001040") +AnnotationAssertion(rdfs:label "intermediate analysis format") +SubClassOf( ) + +# Class: (data stored in database) + +AnnotationAssertion( "NMR:1001107") +AnnotationAssertion(rdfs:label "data stored in database") +SubClassOf( ) + +# Class: (software vendor) + +AnnotationAssertion( "NMR:1001267") +AnnotationAssertion(rdfs:label "software vendor") +SubClassOf( ) + +# Class: (programmer) + +AnnotationAssertion( "NMR:1001268") +AnnotationAssertion(rdfs:label "programmer") +SubClassOf( ) + +# Class: (instrument vendor) + +AnnotationAssertion( "NMR:1001269") +AnnotationAssertion(rdfs:label "instrument vendor") +SubClassOf( ) + +# Class: (lab personnel) + +AnnotationAssertion( "NMR:1001270") +AnnotationAssertion(rdfs:label "lab personnel") +SubClassOf( ) + +# Class: (researcher) + +AnnotationAssertion( "NMR:1001271") +AnnotationAssertion(rdfs:label "researcher") +SubClassOf( ) + +# Class: (analysis software) + +AnnotationAssertion( "NMR:1001456") +AnnotationAssertion(rdfs:label "analysis software") +SubClassOf( ) + +# Class: (data processing software) + +AnnotationAssertion( "NMR:1001457") +AnnotationAssertion(rdfs:label "data processing software") +SubClassOf( ) + +# Class: (data file format) + +AnnotationAssertion( "NMR:1001459") +AnnotationAssertion(rdfs:label "data file format") +SubClassOf( ) + +# Class: (contact phone number) + +AnnotationAssertion( "NMR:1001755") +AnnotationAssertion(rdfs:label "contact phone number") +SubClassOf( ) + +# Class: (contact fax number) + +AnnotationAssertion( "NMR:1001756") +AnnotationAssertion(rdfs:label "contact fax number") +SubClassOf( ) + +# Class: (contact toll-free phone number) + +AnnotationAssertion( "NMR:1001757") +AnnotationAssertion(rdfs:label "contact toll-free phone number") +SubClassOf( ) + +# Class: (Digital Object Identifier (DOI)) + +AnnotationAssertion( "NMR:1001922") +AnnotationAssertion(rdfs:label "Digital Object Identifier (DOI)") +SubClassOf( ) + +# Class: (external reference keyword) + +AnnotationAssertion( "NMR:1001923") +AnnotationAssertion(rdfs:label "external reference keyword") +SubClassOf( ) + +# Class: (journal article keyword) + +AnnotationAssertion( "NMR:1001924") +AnnotationAssertion(rdfs:label "journal article keyword") +SubClassOf( ) + +# Class: (submitter keyword) + +AnnotationAssertion( "NMR:1001925") +AnnotationAssertion(rdfs:label "submitter keyword") +SubClassOf( ) + +# Class: (curator keyword) + +AnnotationAssertion( "NMR:1001926") +AnnotationAssertion(rdfs:label "curator keyword") +SubClassOf( ) + +# Class: (NMR acquisition parameter) + +AnnotationAssertion( "NMR:1001954") +AnnotationAssertion(rdfs:label "NMR acquisition parameter") +SubClassOf( ) + +# Class: (HMDB identifier) + +AnnotationAssertion( "NMR:1002000") +AnnotationAssertion(rdfs:label "HMDB identifier") +SubClassOf( ) + +# Class: (Chenomx software) + +AnnotationAssertion( "NMR:1002001") +AnnotationAssertion(rdfs:label "Chenomx software") +SubClassOf( ) + +# Class: (Chenomx NMR Suite software) + +AnnotationAssertion( "NMR:1002002") +AnnotationAssertion(rdfs:label "Chenomx NMR Suite software") +SubClassOf( ) + +# Class: (Varian FID format) + +AnnotationAssertion( "NMR:1002003") +AnnotationAssertion(rdfs:label "Varian FID format") +SubClassOf( ) + +# Class: (NMR spectrometer file format) + +AnnotationAssertion( "NMR:1002004") +AnnotationAssertion(rdfs:label "NMR spectrometer file format") +SubClassOf( ) + +# Class: (text file) + +AnnotationAssertion( "NMR:1002005") +AnnotationAssertion(rdfs:label "text file") +SubClassOf( ) + +# Class: (acquisition parameter file) + +AnnotationAssertion( "NMR:1002006") +AnnotationAssertion(rdfs:label "acquisition parameter file") +SubClassOf( ) + +# Class: (NMR spectrum) + +AnnotationAssertion( "tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'. + def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. + synonym: NMR spectrum") +AnnotationAssertion( "NMR:1002007") +AnnotationAssertion(rdfs:label "NMR spectrum") +SubClassOf( ) + +# Class: (conversion to nmrML) + +AnnotationAssertion( "NMR:1002008") +AnnotationAssertion(rdfs:label "conversion to nmrML") +SubClassOf( ) + +# Class: (conversion to JCAMP-DX) + +AnnotationAssertion( "NMR:1002009") +AnnotationAssertion(rdfs:label "conversion to JCAMP-DX") +SubClassOf( ) + +# Class: (NMR solvent information) + +AnnotationAssertion( "NMR:1002010") +AnnotationAssertion(rdfs:label "NMR solvent information") +SubClassOf( ) + +# Class: (pH) + +AnnotationAssertion( "NMR:1002011") +AnnotationAssertion(rdfs:label "pH") +SubClassOf( ) + +# Class: (chemical shift reference) + +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/29#issue") +AnnotationAssertion( "NMR:1002013") +AnnotationAssertion(rdfs:label "chemical shift reference") +SubClassOf( ) + +# Class: (binned spectrum descriptor) + +AnnotationAssertion( "NMR:1002014") +AnnotationAssertion(rdfs:label "binned spectrum descriptor") +SubClassOf( ) + +# Class: (bin label) + +AnnotationAssertion( "NMR:1002015") +AnnotationAssertion(rdfs:label "bin label") +SubClassOf( ) + +# Class: (bin start) + +AnnotationAssertion( "NMR:1002016") +AnnotationAssertion(rdfs:label "bin start") +SubClassOf( ) + +# Class: (bin end) + +AnnotationAssertion( "NMR:1002017") +AnnotationAssertion(rdfs:label "bin end") +SubClassOf( ) + +# Class: (bin area) + +AnnotationAssertion( "NMR:1002018") +AnnotationAssertion(rdfs:label "bin area") +SubClassOf( ) + +# Class: (assigned chemical compound name) + +AnnotationAssertion( "NMR:1002020") +AnnotationAssertion(rdfs:label "assigned chemical compound name") +SubClassOf( ) + +# Class: (assigned chemical compound concentration) + +AnnotationAssertion( "NMR:1002021") +AnnotationAssertion(rdfs:label "assigned chemical compound concentration") +SubClassOf( ) + +# Class: (Hilbert transformation based scaling) + +AnnotationAssertion(rdfs:label "Hilbert transformation based scaling"@en) +SubClassOf( ) + +# Class: (optional part of NMR instrument) + +AnnotationAssertion(rdfs:label "optional part of NMR instrument") +SubClassOf( ) + +# Class: (autosampler) + +AnnotationAssertion(rdfs:label "autosampler") +SubClassOf( ) + +# Class: (multiplicity feature) + +AnnotationAssertion( "http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm") +AnnotationAssertion(rdfs:label "multiplicity feature") +SubClassOf( ) + +# Class: (projected spectrum) + +AnnotationAssertion(rdfs:label "projected spectrum") +SubClassOf( ) + +# Class: (bucketed spectrum) + +AnnotationAssertion(rdfs:label "bucketed spectrum") +SubClassOf( ) + +# Class: (peak-picked spectrum) + +AnnotationAssertion(rdfs:label "peak-picked spectrum") +SubClassOf( ) + +# Class: (cardinal part of NMR instrument) + +AnnotationAssertion(rdfs:label "cardinal part of NMR instrument") +SubClassOf( ) + +# Class: (acquisition computer) + +AnnotationAssertion(rdfs:label "acquisition computer") +SubClassOf( ) + +# Class: (NMR probe) + +AnnotationAssertion(rdfs:label "NMR probe") +SubClassOf( ) + +# Class: (console) + +AnnotationAssertion(rdfs:label "console") +SubClassOf( ) + +# Class: (number of acquisition data points) + +AnnotationAssertion(rdfs:label "number of acquisition data points") +SubClassOf( ) + +# Class: (hadamard frequency) + +AnnotationAssertion(rdfs:label "hadamard frequency") +SubClassOf( ) + +# Class: (projection axis) + +AnnotationAssertion(rdfs:label "projection axis") +SubClassOf( ) + +# Class: (ninety degree pulse duration) + +AnnotationAssertion(rdfs:label "ninety degree pulse duration") +SubClassOf( ) + +# Class: (dwell time) + +AnnotationAssertion(rdfs:label "dwell time") +SubClassOf( ) + +# Class: (sample temperature in autosampler) + +AnnotationAssertion(rdfs:label "sample temperature in autosampler") +SubClassOf( ) + +# Class: (sample temperature in magnet) + +AnnotationAssertion(rdfs:label "sample temperature in magnet") +SubClassOf( ) + +# Class: (irradiation frequency) + +AnnotationAssertion(rdfs:label "irradiation frequency") +SubClassOf( ) + +# Class: (field strength) + +AnnotationAssertion(rdfs:label "field strength") +SubClassOf( ) + +# Class: (spinning rate) + +AnnotationAssertion(rdfs:label "spinning rate") +SubClassOf( ) + +# Class: (decoupled nucleus flag) + +AnnotationAssertion(rdfs:label "decoupled nucleus flag") +SubClassOf( ) + +# Class: (buffer information) + +AnnotationAssertion(rdfs:label "buffer information") +SubClassOf( ) + +# Class: (calibration compound) + +AnnotationAssertion(rdfs:label "calibration compound") +SubClassOf( ) + +# Class: (chemical shift standard) + +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/31") +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/33") +AnnotationAssertion(rdfs:label "chemical shift standard") +SubClassOf( ) + +# Class: (quality check compound signal) + +AnnotationAssertion(rdfs:label "quality check compound signal") +SubClassOf( ) + +# Class: (NMR pulse sequence) + +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/40") +AnnotationAssertion(rdfs:label "NMR pulse sequence") +SubClassOf( ) + +# Class: (frequency domain data processing) + +AnnotationAssertion(rdfs:label "frequency domain data processing"@en) +SubClassOf( ) + +# Class: (time domain data processing) + +AnnotationAssertion(rdfs:label "time domain data processing"@en) +SubClassOf( ) + +# Class: (NMR data processing) + +AnnotationAssertion(rdfs:label "NMR data processing") +SubClassOf( ) + +# Class: (non-fourier FID transformation) + +AnnotationAssertion(rdfs:label "non-fourier FID transformation") +SubClassOf( ) + +# Class: (data encoding) + +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/37") +AnnotationAssertion(rdfs:label "data encoding") +SubClassOf( ) + +# Class: (G matrix fourier transform projection) + +AnnotationAssertion(rdfs:label "G matrix fourier transform projection") +SubClassOf( ) + +# Class: (time proportional phase incrementation) + +AnnotationAssertion(rdfs:label "time proportional phase incrementation") +SubClassOf( ) + +# Class: (states-time proportional phase incrementation) + +AnnotationAssertion(rdfs:label "states-time proportional phase incrementation") +SubClassOf( ) + +# Class: (Hadamard encoding) + +AnnotationAssertion(rdfs:label "Hadamard encoding") +SubClassOf( ) + +# Class: (Frydman encoding) + +AnnotationAssertion(rdfs:label "Frydman encoding") +SubClassOf( ) + +# Class: (echo anti-echo coherence selection) + +AnnotationAssertion(rdfs:label "echo anti-echo coherence selection") +SubClassOf( ) + +# Class: (NMR instrument) + +AnnotationAssertion(rdfs:label "NMR instrument") +SubClassOf( ) + +# Class: (NMR instrument acquisition parameter set) + +AnnotationAssertion(rdfs:label "NMR instrument acquisition parameter set") +SubClassOf( ) + +# Class: (data transformation) + +AnnotationAssertion(rdfs:label "data transformation"@en) +SubClassOf( ) + +# Class: (normalisation) + +AnnotationAssertion( "Philippe Rocca Serra") +AnnotationAssertion( "http://pubs.acs.org/doi/pdf/10.1021/ac0519312 + +10.1021/ac0519312 + +Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets + +Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * +Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K.") +AnnotationAssertion( "http://stats.stackexchange.com/questions/35591/normalization-vs-scaling") +AnnotationAssertion(rdfs:label "normalisation") +SubClassOf( ) + +# Class: (pre-acquisition water suppression) + +AnnotationAssertion(rdfs:label "pre-acquisition water suppression") +SubClassOf( ) + +# Class: (window function for apodization) + +AnnotationAssertion( "A function applied to a FID to increase the signal-to-noise ratio or the resolution.") +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/39") +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/67") +AnnotationAssertion(rdfs:label "window function for apodization") +SubClassOf( ) + +# Class: (exponential multiplication window function) + +AnnotationAssertion( "The exponential function used to multiply a FID by to produce a desitred amount of line broadening.") +AnnotationAssertion(rdfs:label "exponential multiplication window function") +SubClassOf( ) + +# Class: (Gaussian window function) + +AnnotationAssertion(rdfs:label "Gaussian window function") +SubClassOf( ) + +# Class: (sine window function) + +AnnotationAssertion(rdfs:label "sine window function") +SubClassOf( ) + +# Class: (sine squared window) + +AnnotationAssertion(rdfs:label "sine squared window") +SubClassOf( ) + +# Class: (spectral denoising) + +AnnotationAssertion(rdfs:label "spectral denoising") +SubClassOf( ) + +# Class: (baseline correction) + +AnnotationAssertion(rdfs:label "baseline correction") +SubClassOf( ) + +# Class: (spectral projection) + +AnnotationAssertion(rdfs:label "spectral projection") +SubClassOf( ) + +# Class: (maximum intensity projection) + +AnnotationAssertion(rdfs:label "maximum intensity projection") +SubClassOf( ) + +# Class: (summation projection) + +AnnotationAssertion(rdfs:label "summation projection") +SubClassOf( ) + +# Class: (zero order phase correction) + +AnnotationAssertion(rdfs:label "zero order phase correction") +SubClassOf( ) + +# Class: (first order phase correction) + +AnnotationAssertion(rdfs:label "first order phase correction") +SubClassOf( ) + +# Class: (symmetrisation) + +AnnotationAssertion(rdfs:label "symmetrisation") +SubClassOf( ) + +# Class: (acquisition nucleus) + +AnnotationAssertion(rdfs:label "acquisition nucleus") +SubClassOf( ) + +# Class: (quality check peak feature) + +AnnotationAssertion(rdfs:label "quality check peak feature") +SubClassOf( ) + +# Class: (number of scans) + +AnnotationAssertion(rdfs:label "number of scans") +SubClassOf( ) + +# Class: (number of steady state scans) + +AnnotationAssertion(rdfs:label "number of steady state scans") +SubClassOf( ) + +# Class: (atom environment encoding) + +AnnotationAssertion(rdfs:label "atom environment encoding") +SubClassOf( ) + +# Class: (relaxation delay) + +AnnotationAssertion(rdfs:label "relaxation delay") +SubClassOf( ) + +# Class: (x-axis unit) + +AnnotationAssertion(rdfs:label "x-axis unit") +SubClassOf( ) + +# Class: (y-axis unit) + +AnnotationAssertion(rdfs:label "y-axis unit") +SubClassOf( ) + +# Class: (additional axis unit) + +AnnotationAssertion(rdfs:label "additional axis unit") +SubClassOf( ) + +# Class: (x start value) + +AnnotationAssertion(rdfs:label "x start value") +SubClassOf( ) + +# Class: (x end value) + +AnnotationAssertion(rdfs:label "x end value") +SubClassOf( ) + +# Class: (window function parameter) + +AnnotationAssertion(rdfs:label "window function parameter") +SubClassOf( ) + +# Class: (line broadening) + +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. + +Hans J. Reich 2015, University of Wisconsin") +AnnotationAssertion(rdfs:label "line broadening") +SubClassOf( ) + +# Class: (line sharpening) + +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. + +Hans J. Reich 2015, University of Wisconsin") +AnnotationAssertion(rdfs:label "line sharpening") +SubClassOf( ) + +# Class: (parameter) + +AnnotationAssertion(rdfs:label "parameter") +SubClassOf( ) + +# Class: (NMR spectral projection parameter set) + +AnnotationAssertion(rdfs:label "NMR spectral projection parameter set") +SubClassOf( ) + +# Class: (NMR data post-processing parameter set) + +AnnotationAssertion(rdfs:label "NMR data post-processing parameter set") +SubClassOf( ) + +# Class: (NMR quality check parameter set) + +AnnotationAssertion(rdfs:label "NMR quality check parameter set") +SubClassOf( ) + +# Class: (post-acquisition water suppression) + +AnnotationAssertion(rdfs:label "post-acquisition water suppression") +SubClassOf( ) + +# Class: (hankel singular value decomposition) + +AnnotationAssertion(rdfs:label "hankel singular value decomposition") +SubClassOf( ) + +# Class: (convolution) + +AnnotationAssertion(rdfs:label "convolution") +SubClassOf( ) + +# Class: (polynomial fitting) + +AnnotationAssertion(rdfs:label "polynomial fitting") +SubClassOf( ) + +# Class: (WaveWat) + +AnnotationAssertion(rdfs:label "WaveWat") +SubClassOf( ) + +# Class: (NMR data pre-processing parameter set) + +AnnotationAssertion(rdfs:label "NMR data pre-processing parameter set") +SubClassOf( ) + +# Class: (NMR quality check) + +AnnotationAssertion(rdfs:label "NMR quality check") +SubClassOf( ) + +# Class: (reference) + +AnnotationAssertion(rdfs:label "reference") +SubClassOf( ) + +# Class: (FID file) + +AnnotationAssertion(rdfs:label "FID file") +SubClassOf( ) + +# Class: (pulse sequence literature reference) + +AnnotationAssertion(rdfs:label "pulse sequence literature reference") +SubClassOf( ) + +# Class: (shaped pulse file) + +AnnotationAssertion(rdfs:label "shaped pulse file") +SubClassOf( ) + +# Class: (pulse sequence file) + +AnnotationAssertion(rdfs:label "pulse sequence file") +SubClassOf( ) + +# Class: (processing parameter file) + +AnnotationAssertion(rdfs:label "processing parameter file") +SubClassOf( ) + +# Class: (NMR sample identifier) + +AnnotationAssertion(rdfs:label "NMR sample identifier") +SubClassOf( ) + +# Class: (NMR quality check descriptor) + +AnnotationAssertion(rdfs:label "NMR quality check descriptor") +SubClassOf( ) + +# Class: (NMR sample) + +AnnotationAssertion(rdfs:label "NMR sample") +SubClassOf( ) + +# Class: (sample introduction parameter) + +AnnotationAssertion(rdfs:label "sample introduction parameter") +SubClassOf( ) + +# Class: (magic angle spinning rotor) + +AnnotationAssertion(rdfs:label "magic angle spinning rotor") +SubClassOf( ) + +# Class: (flow probe) + +AnnotationAssertion(rdfs:label "flow probe") +SubClassOf( ) + +# Class: (NMR sample tube) + +AnnotationAssertion( "The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.") +AnnotationAssertion( "https://github.com/nmrML/nmrML/issues/54") +AnnotationAssertion(rdfs:label "NMR sample tube") +SubClassOf( ) + +# Class: (spectrum pre-processing software) + +AnnotationAssertion(rdfs:label "spectrum pre-processing software") +SubClassOf( ) + +# Class: (spectrum post-processing software) + +AnnotationAssertion(rdfs:label "spectrum post-processing software") +SubClassOf( ) + +# Class: (peak picking) + +AnnotationAssertion(rdfs:label "peak picking") +SubClassOf( ) + +# Class: (bucketing) + +AnnotationAssertion(rdfs:label "bucketing") +SubClassOf( ) + +# Class: (presat pulse sequence) + +AnnotationAssertion(rdfs:label "presat pulse sequence") +SubClassOf( ) + +# Class: (water suppression enhanced through T1 effects) + +AnnotationAssertion(rdfs:label "water suppression enhanced through T1 effects") +SubClassOf( ) + +# Class: (nuclear overhauser and exchange spectroscopy-presat) + +AnnotationAssertion(rdfs:label "nuclear overhauser and exchange spectroscopy-presat") +SubClassOf( ) + +# Class: (watergate) + +AnnotationAssertion(rdfs:label "watergate") +SubClassOf( ) + +# Class: (coherence pathway rejection) + +AnnotationAssertion(rdfs:label "coherence pathway rejection") +SubClassOf( ) + +# Class: (flip-back watergate) + +AnnotationAssertion(rdfs:label "flip-back watergate") +SubClassOf( ) + +# Class: (jump and return pulse sequence) + +AnnotationAssertion(rdfs:label "jump and return pulse sequence") +SubClassOf( ) + +# Class: (jump and return 1-1) + +AnnotationAssertion(rdfs:label "jump and return 1-1") +SubClassOf( ) + +# Class: (jump and return 1-3-3-1) + +AnnotationAssertion(rdfs:label "jump and return 1-3-3-1") +SubClassOf( ) + +# Class: (1D spectrum) + +AnnotationAssertion(rdfs:label "1D spectrum") +SubClassOf( ) + +# Class: (2D spectrum) + +AnnotationAssertion(rdfs:label "2D spectrum") +SubClassOf( ) + +# Class: (1D NMR acquisition parameter set) + +AnnotationAssertion(rdfs:label "1D NMR acquisition parameter set") +SubClassOf( ) + +# Class: (2D NMR acquisition parameter set) + +AnnotationAssertion(rdfs:label "2D NMR acquisition parameter set") +SubClassOf( ) + +# Class: (carr purcell meiboom gill pulse sequence) + +AnnotationAssertion(rdfs:label "carr purcell meiboom gill pulse sequence") +SubClassOf( ) + +# Class: ( total correlation spectroscopy pulse sequence) + +AnnotationAssertion(rdfs:label " total correlation spectroscopy pulse sequence") +SubClassOf( ) + +# Class: (1D pulse sequence) + +AnnotationAssertion(rdfs:label "1D pulse sequence") +SubClassOf( ) + +# Class: (J-resolved pulse sequence) + +AnnotationAssertion(rdfs:label "J-resolved pulse sequence") +SubClassOf( ) + +# Class: (hadamard total correlation spectroscopy pulse sequence) + +AnnotationAssertion(rdfs:label "hadamard total correlation spectroscopy pulse sequence") +SubClassOf( ) + +# Class: (diffusion edited pulse sequence) + +AnnotationAssertion(rdfs:label "diffusion edited pulse sequence") +SubClassOf( ) + +# Class: (NMR magnet) + +AnnotationAssertion(rdfs:label "NMR magnet") +SubClassOf( ) + +# Class: (Bruker NMR magnet) + +AnnotationAssertion(rdfs:label "Bruker NMR magnet") +SubClassOf( ) + +# Class: (UltraShield) + +AnnotationAssertion(rdfs:label "UltraShield") +SubClassOf( ) + +# Class: (Ultrastabilized) + +AnnotationAssertion(rdfs:label "Ultrastabilized") +SubClassOf( ) + +# Class: (US 2) + +AnnotationAssertion(rdfs:label "US 2") +SubClassOf( ) + +# Class: (UltraShield Plus) + +AnnotationAssertion(rdfs:label "UltraShield Plus") +SubClassOf( ) + +# Class: (Bruker CryoProbe) + +AnnotationAssertion(rdfs:label "Bruker CryoProbe") +SubClassOf( ) +SubClassOf( ) + +# Class: (high resolution magic angle spin probe) + +AnnotationAssertion(rdfs:label "high resolution magic angle spin probe") +SubClassOf( ) + +# Class: (solid magic angle spinning probe) + +AnnotationAssertion(rdfs:label "solid magic angle spinning probe") +SubClassOf( ) + +# Class: (1mm MicroProbe) + +AnnotationAssertion(rdfs:label "1mm MicroProbe") +SubClassOf( ) + +# Class: (flow high resolution probe) + +AnnotationAssertion(rdfs:label "flow high resolution probe") +SubClassOf( ) + +# Class: (NMR instrument parameter set) + +AnnotationAssertion(rdfs:label "NMR instrument parameter set") +SubClassOf( ) + +# Class: (AVANCE II spectrometer) + +AnnotationAssertion(rdfs:label "AVANCE II spectrometer") +SubClassOf( ) + +# Class: (Bruker NMR instrument) + +AnnotationAssertion(rdfs:label "Bruker NMR instrument") +SubClassOf( ) + +# Class: (Metabolic Profiler instrument) + +AnnotationAssertion(rdfs:label "Metabolic Profiler instrument") +SubClassOf( ) + +# Class: (Hyphenated NMR instrument) + +AnnotationAssertion(rdfs:label "Hyphenated NMR instrument") +SubClassOf( ) + +# Class: (Capillary LC-NMR) + +AnnotationAssertion(rdfs:label "Capillary LC-NMR") +SubClassOf( ) + +# Class: (NMR Case) + +AnnotationAssertion(rdfs:label "NMR Case") +SubClassOf( ) + +# Class: (NMR tube washing system) + +AnnotationAssertion(rdfs:label "NMR tube washing system") +SubClassOf( ) + +# Class: (Bruker AutoClean) + +AnnotationAssertion(rdfs:label "Bruker AutoClean") +SubClassOf( ) + +# Class: (Bruker BEST NMR) + +AnnotationAssertion(rdfs:label "Bruker BEST NMR") +SubClassOf( ) + +# Class: (SampleRail) + +AnnotationAssertion(rdfs:label "SampleRail") +SubClassOf( ) + +# Class: (SampleJet) + +AnnotationAssertion(rdfs:label "SampleJet") +SubClassOf( ) + +# Class: (Bruker autosampler) + +AnnotationAssertion(rdfs:label "Bruker autosampler") +SubClassOf( ) + +# Class: (B-ACS) + +AnnotationAssertion(rdfs:label "B-ACS") +SubClassOf( ) + +# Class: (Bruker MATCH) + +AnnotationAssertion(rdfs:label "Bruker MATCH") +SubClassOf( ) + +# Class: (NMR sample holder) + +AnnotationAssertion(rdfs:label "NMR sample holder") +SubClassOf( ) + +# Class: (NMR software) + +AnnotationAssertion(rdfs:label "NMR software") +SubClassOf( ) + +# Class: (Bruker NMR software) + +AnnotationAssertion(rdfs:label "Bruker NMR software") +SubClassOf( ) + +# Class: (Bruker TopSpin software) + +AnnotationAssertion(rdfs:label "Bruker TopSpin software") +SubClassOf( ) + +# Class: (SampleTrack software) + +AnnotationAssertion(rdfs:label "SampleTrack software") +SubClassOf( ) + +# Class: (Paravision software) + +AnnotationAssertion(rdfs:label "Paravision software") +SubClassOf( ) + +# Class: (AURELIA software) + +AnnotationAssertion(rdfs:label "AURELIA software") +SubClassOf( ) + +# Class: (AUREMOL software) + +AnnotationAssertion(rdfs:label "AUREMOL software") +SubClassOf( ) + +# Class: (AMIX VIEWER & AMIX-TOOLS) + +AnnotationAssertion(rdfs:label "AMIX VIEWER & AMIX-TOOLS") +SubClassOf( ) + +# Class: (high resolution probe) + +AnnotationAssertion(rdfs:label "high resolution probe") +SubClassOf( ) + +# Class: (high resolution probe with ATM) + +AnnotationAssertion(rdfs:label "high resolution probe with ATM") +SubClassOf( ) + +# Class: (micro imaging probe) + +AnnotationAssertion(rdfs:label "micro imaging probe") +SubClassOf( ) + +# Class: (JEOL NMR instrument) + +AnnotationAssertion(rdfs:label "JEOL NMR instrument") +SubClassOf( ) + +# Class: (JNM-ECX Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECX Series FT NMR instrument") +SubClassOf( ) + +# Class: (JNM-ECA Series FT NMR instrument) + +AnnotationAssertion(rdfs:label "JNM-ECA Series FT NMR instrument") +SubClassOf( ) + +# Class: (JEOL NMR software) + +AnnotationAssertion(rdfs:label "JEOL NMR software") +SubClassOf( ) + +# Class: (Delta NMR software) + +AnnotationAssertion(rdfs:label "Delta NMR software") +SubClassOf( ) + +# Class: (Bruker NMR probe) + +AnnotationAssertion(rdfs:label "Bruker NMR probe") +SubClassOf( ) + +# Class: (JEOL NMR probe) + +AnnotationAssertion(rdfs:label "JEOL NMR probe") +SubClassOf( ) + +# Class: (CapNMR probe) + +AnnotationAssertion(rdfs:label "CapNMR probe") +SubClassOf( ) + +# Class: (Varian NMR instrument) + +AnnotationAssertion(rdfs:label "Varian NMR instrument") +SubClassOf( ) + +# Class: (Varian MERCURY) + +AnnotationAssertion(rdfs:label "Varian MERCURY") +SubClassOf( ) + +# Class: (Varian INOVA) + +AnnotationAssertion(rdfs:label "Varian INOVA") +SubClassOf( ) + +# Class: (Varian UNITY) + +AnnotationAssertion(rdfs:label "Varian UNITY") +SubClassOf( ) + +# Class: (Varian VXR) + +AnnotationAssertion(rdfs:label "Varian VXR") +SubClassOf( ) + +# Class: (Varian GEMINI) + +AnnotationAssertion(rdfs:label "Varian GEMINI") +SubClassOf( ) + +# Class: (AMX instrument) + +AnnotationAssertion(rdfs:label "AMX instrument") +SubClassOf( ) + +# Class: (AC instrument) + +AnnotationAssertion(rdfs:label "AC instrument") +SubClassOf( ) + +# Class: (liquid NMR probe) + +AnnotationAssertion(rdfs:label "liquid NMR probe") +SubClassOf( ) + +# Class: (solid NMR probe) + +AnnotationAssertion(rdfs:label "solid NMR probe") +SubClassOf( ) + +# Class: (NMR imaging probe) + +AnnotationAssertion(rdfs:label "NMR imaging probe") +SubClassOf( ) + +# Class: (tecmag console) + +AnnotationAssertion(rdfs:label "tecmag console") +SubClassOf( ) + +# Class: (DISCOVERY console) + +AnnotationAssertion(rdfs:label "DISCOVERY console") +SubClassOf( ) + +# Class: (tecmag EAGLE probe) + +AnnotationAssertion(rdfs:label "tecmag EAGLE probe") +SubClassOf( ) + +# Class: (APOLLO console) + +AnnotationAssertion(rdfs:label "APOLLO console") +SubClassOf( ) + +# Class: (tecmag NMR instrument) + +AnnotationAssertion(rdfs:label "tecmag NMR instrument") +SubClassOf( ) + +# Class: (CAT) + +AnnotationAssertion(rdfs:label "CAT") +SubClassOf( ) + +# Class: (magnetic field strength) + +AnnotationAssertion(rdfs:label "magnetic field strength") +SubClassOf( ) + +# Class: (vendor) + +AnnotationAssertion(rdfs:label "vendor") +SubClassOf( ) + +# Class: (NMR instrument manufacturer) + +AnnotationAssertion(rdfs:label "NMR instrument manufacturer") +SubClassOf( ) + +# Class: (Bruker) + +AnnotationAssertion(rdfs:label "Bruker") +SubClassOf( ) + +# Class: (Varian) + +AnnotationAssertion(rdfs:label "Varian") +SubClassOf( ) + +# Class: (JEOL) + +AnnotationAssertion(rdfs:label "JEOL") +SubClassOf( ) + +# Class: (MR Resources) + +AnnotationAssertion(rdfs:label "MR Resources") +SubClassOf( ) + +# Class: (tecmag) + +AnnotationAssertion(rdfs:label "tecmag") +SubClassOf( ) + +# Class: (sample temperature information) + +AnnotationAssertion(rdfs:label "sample temperature information") +SubClassOf( ) + +# Class: (Doty Scientific) + +AnnotationAssertion(rdfs:label "Doty Scientific") +SubClassOf( ) + +# Class: (Wilmad) + +AnnotationAssertion(rdfs:label "Wilmad") +SubClassOf( ) + +# Class: (JS Research) + +AnnotationAssertion(rdfs:label "JS Research") +SubClassOf( ) + +# Class: (data file) + +AnnotationAssertion(rdfs:label "data file") +SubClassOf( ) + +# Class: (Acorn NMR Inc) + +AnnotationAssertion(rdfs:label "Acorn NMR Inc") +SubClassOf( ) + +# Class: (liquid chromatography NMR) + +AnnotationAssertion(rdfs:label "liquid chromatography NMR") +SubClassOf( ) + +# Class: (LC MS NMR) + +AnnotationAssertion(rdfs:label "LC MS NMR") +SubClassOf( ) + +# Class: (solid phase extraction NMR) + +AnnotationAssertion(rdfs:label "solid phase extraction NMR") +SubClassOf( ) + +# Class: (Capillary LC-NMR) + +AnnotationAssertion(rdfs:label "Capillary LC-NMR") +SubClassOf( ) + +# Class: (direct detection probe) + +AnnotationAssertion(rdfs:label "direct detection probe") +SubClassOf( ) + +# Class: (indirect detection probe) + +AnnotationAssertion(rdfs:label "indirect detection probe") +SubClassOf( ) + +# Class: (continuous wave NMR) + +AnnotationAssertion(rdfs:label "continuous wave NMR") +SubClassOf( ) + +# Class: (fourier transformation NMR instrument) + +AnnotationAssertion(rdfs:label "fourier transformation NMR instrument") +SubClassOf( ) + +# Class: (NMR software data format) + +AnnotationAssertion(rdfs:label "NMR software data format") +SubClassOf( ) + +# Class: (ChemMagnetics format) + +AnnotationAssertion(rdfs:label "ChemMagnetics format") +SubClassOf( ) + +# Class: (GE Omega format) + +AnnotationAssertion(rdfs:label "GE Omega format") +SubClassOf( ) + +# Class: (JEOL Lambda format) + +AnnotationAssertion(rdfs:label "JEOL Lambda format") +SubClassOf( ) + +# Class: (JEOL Alpha format) + +AnnotationAssertion(rdfs:label "JEOL Alpha format") +SubClassOf( ) + +# Class: (Jeol Delta format) + +AnnotationAssertion(rdfs:label "Jeol Delta format") +SubClassOf( ) + +# Class: (JEOL generic format) + +AnnotationAssertion(rdfs:label "JEOL generic format") +SubClassOf( ) + +# Class: (JEOL AL95 format) + +AnnotationAssertion(rdfs:label "JEOL AL95 format") +SubClassOf( ) + +# Class: (JEOL EX format) + +AnnotationAssertion(rdfs:label "JEOL EX format") +SubClassOf( ) + +# Class: (TecMag format) + +AnnotationAssertion(rdfs:label "TecMag format") +SubClassOf( ) + +# Class: (Varian VNMR format) + +AnnotationAssertion(rdfs:label "Varian VNMR format") +SubClassOf( ) + +# Class: (Galactic format) + +AnnotationAssertion(rdfs:label "Galactic format") +SubClassOf( ) + +# Class: (Felix format) + +AnnotationAssertion(rdfs:label "Felix format") +SubClassOf( ) + +# Class: (JCAMP DX format) + +AnnotationAssertion(rdfs:label "JCAMP DX format") +SubClassOf( ) + +# Class: (Lybrics format) + +AnnotationAssertion(rdfs:label "Lybrics format") +SubClassOf( ) + +# Class: (Nuts format) + +AnnotationAssertion(rdfs:label "Nuts format") +SubClassOf( ) + +# Class: (MACNMR format) + +AnnotationAssertion(rdfs:label "MACNMR format") +SubClassOf( ) + +# Class: (Nicolet GE/QE-300 format) + +AnnotationAssertion(rdfs:label "Nicolet GE/QE-300 format") +SubClassOf( ) + +# Class: (multiplet feature) + +AnnotationAssertion(rdfs:label "multiplet feature") +SubClassOf( ) + +# Class: (ThermoMattson) + +AnnotationAssertion(rdfs:label "ThermoMattson") +SubClassOf( ) + +# Class: (FOSS) + +AnnotationAssertion(rdfs:label "FOSS") +SubClassOf( ) + +# Class: (Jasco) + +AnnotationAssertion(rdfs:label "Jasco") +SubClassOf( ) + +# Class: (Agilent Technologies) + +AnnotationAssertion(rdfs:label "Agilent Technologies") +SubClassOf( ) + +# Class: (micromass) + +AnnotationAssertion(rdfs:label "micromass") +SubClassOf( ) + +# Class: (Waters) + +AnnotationAssertion(rdfs:label "Waters") +SubClassOf( ) + +# Class: (ThermoNicolet) + +AnnotationAssertion(rdfs:label "ThermoNicolet") +SubClassOf( ) + +# Class: (Perkin Elmer) + +AnnotationAssertion(rdfs:label "Perkin Elmer") +SubClassOf( ) + +# Class: (OceanOptics) + +AnnotationAssertion(rdfs:label "OceanOptics") +SubClassOf( ) + +# Class: (ThermoFinnigan) + +AnnotationAssertion(rdfs:label "ThermoFinnigan") +SubClassOf( ) + +# Class: (Applied Biosystems) + +AnnotationAssertion(rdfs:label "Applied Biosystems") +SubClassOf( ) + +# Class: (TX) + +AnnotationAssertion(rdfs:label "TX") +SubClassOf( ) + +# Class: (Net CDF format) + +AnnotationAssertion(rdfs:label "Net CDF format") +SubClassOf( ) + +# Class: (Bruker DISNMR format) + +AnnotationAssertion(rdfs:label "Bruker DISNMR format") +SubClassOf( ) + +# Class: (Bruker UXNMR/XWIN-NMR format) + +AnnotationAssertion(rdfs:label "Bruker UXNMR/XWIN-NMR format") +SubClassOf( ) + +# Class: (Bruker WIN NMR format) + +AnnotationAssertion(rdfs:label "Bruker WIN NMR format") +SubClassOf( ) + +# Class: (acdlabs) + +AnnotationAssertion(rdfs:label "acdlabs") +SubClassOf( ) + +# Class: (software development) + +AnnotationAssertion( "A planned process that has specified output a software product and that involves the creation of source code."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "http://en.wikipedia.org/wiki/Software_development") +AnnotationAssertion( "A planned process resulting in a software product involving the creation of source code."@en) +AnnotationAssertion(rdfs:label "software development"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))) +SubClassOf( ) + +# Class: (dataset creating) + +AnnotationAssertion( "creating a data set"@en) +AnnotationAssertion( "A planned process that has a data set as its specified output."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "data set creation"@en) +AnnotationAssertion( "dataset creation"@en) +AnnotationAssertion(rdfs:label "dataset creating"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (entity) + +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (spatial region) + +AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) +AnnotationAssertion(Annotation( ) "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])"@en) +AnnotationAssertion(Annotation( ) "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ") +AnnotationAssertion(rdfs:label "spatial region"@en) +SubClassOf( ) + +# Class: (two-dimensional spatial region) + +AnnotationAssertion( "an infinitely thin plane in space."@en) +AnnotationAssertion( "the surface of a sphere-shaped part of space"@en) +AnnotationAssertion(Annotation( ) "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] ") +AnnotationAssertion(rdfs:label "two-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (process) + +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (zero-dimensional spatial region) + +AnnotationAssertion(Annotation( ) "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] ") +AnnotationAssertion(rdfs:label "zero-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (one-dimensional spatial region) + +AnnotationAssertion( "an edge of a cube-shaped portion of space."@en) +AnnotationAssertion(Annotation( ) "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] ") +AnnotationAssertion(rdfs:label "one-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (object) + +AnnotationAssertion( "atom"@en) +AnnotationAssertion( "cell"@en) +AnnotationAssertion( "cells and organisms"@en) +AnnotationAssertion( "engineered artifacts"@en) +AnnotationAssertion( "grain of sand"@en) +AnnotationAssertion( "molecule"@en) +AnnotationAssertion( "organelle"@en) +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "planet"@en) +AnnotationAssertion( "solid portions of matter"@en) +AnnotationAssertion( "star"@en) +AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) +AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) +AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) +AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) +AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) +AnnotationAssertion(Annotation( ) "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])"@en) +AnnotationAssertion(rdfs:label "object"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (function) + +AnnotationAssertion( "the function of a hammer to drive in nails"@en) +AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) +AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) +AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) +AnnotationAssertion(Annotation( ) "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ") +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial entity) + +AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (electron) + +AnnotationAssertion( "Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.") +AnnotationAssertion( "CHEBI:10545") +AnnotationAssertion(rdfs:label "electron") +SubClassOf( ) + +# Class: (primary nitroalkane) + +AnnotationAssertion( "A nitroalkane in which the nitro group is attached to a terminal carbon. Major microspecies at pH 7.3.") +AnnotationAssertion( "CHEBI:133972") +AnnotationAssertion(rdfs:label "primary nitroalkane") +SubClassOf( ) + +# Class: (volatile organic compound) + +AnnotationAssertion( "Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.") +AnnotationAssertion( "CHEBI:134179") +AnnotationAssertion(rdfs:label "volatile organic compound") +SubClassOf( ) + +# Class: (aci-nitro compound) + +AnnotationAssertion( "Organonitrogen compounds that have the general structure R(1)(R(2))C=N(O)OH (R(1),R(2) = H, organyl). They are tautomers of C-nitro compounds.") +AnnotationAssertion( "CHEBI:136622") +AnnotationAssertion(rdfs:label "aci-nitro compound") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (secondary ammonium ion) + +AnnotationAssertion( "An organic cation obtained by protonation of any secondary amino compound; major species at pH 7.3.") +AnnotationAssertion( "CHEBI:137419") +AnnotationAssertion(rdfs:label "secondary ammonium ion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (inorganic acid) + +AnnotationAssertion( "A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.") +AnnotationAssertion( "CHEBI:138103") +AnnotationAssertion(rdfs:label "inorganic acid") +SubClassOf( ) + +# Class: (gas molecular entity) + +AnnotationAssertion( "Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).") +AnnotationAssertion( "CHEBI:138675") +AnnotationAssertion(rdfs:label "gas molecular entity") +SubClassOf( ) + +# Class: (isotopically modified compound) + +AnnotationAssertion( "Any molecular entity in which the isotopic ratio of nuclides for at least one element deviates measurably from that occurring in nature. The term includes both isotopically substituted compounds (in which essentially all the molecules of the compound have only the indicated nuclide(s) at each designated position) and isotopically labeled compounds (a formal mixture of an isotopically unmodified compound with one or more analogous isotopically substituted compound(s).") +AnnotationAssertion( "CHEBI:139358") +AnnotationAssertion(rdfs:label "isotopically modified compound") +SubClassOf( ) + +# Class: (carbamate) + +AnnotationAssertion( "CHEBI:13941") +AnnotationAssertion(rdfs:label "carbamate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxime anion) + +AnnotationAssertion( "A organic ion resulting from the deprotonation of the hydroxy group of any oxime.") +AnnotationAssertion( "CHEBI:142513") +AnnotationAssertion(rdfs:label "oxime anion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (acceptor) + +AnnotationAssertion( "A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.") +AnnotationAssertion( "CHEBI:15339") +AnnotationAssertion(rdfs:label "acceptor") +SubClassOf( ) + +# Class: (acetic acid) + +AnnotationAssertion( "A simple monocarboxylic acid containing two carbons.") +AnnotationAssertion( "CHEBI:15366") +AnnotationAssertion(rdfs:label "acetic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (water) + +AnnotationAssertion( "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms") +AnnotationAssertion( "CHEBI:15377") +AnnotationAssertion(rdfs:label "water") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycine) + +AnnotationAssertion( "The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.") +AnnotationAssertion( "CHEBI:15428") +AnnotationAssertion(rdfs:label "glycine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (polypeptide) + +AnnotationAssertion( "A peptide containing ten or more amino acid residues.") +AnnotationAssertion( "CHEBI:15841") +AnnotationAssertion(rdfs:label "polypeptide") +SubClassOf( ) +SubClassOf( ) + +# Class: (biotin) + +AnnotationAssertion( "An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.") +AnnotationAssertion( "CHEBI:15956") +AnnotationAssertion(rdfs:label "biotin") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (polynucleotide) + +AnnotationAssertion( "A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.") +AnnotationAssertion( "CHEBI:15986") +AnnotationAssertion(rdfs:label "polynucleotide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ammonia) + +AnnotationAssertion( "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.") +AnnotationAssertion( "CHEBI:16134") +AnnotationAssertion(rdfs:label "ammonia") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (methane) + +AnnotationAssertion( "A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. It is a colourless, odourless, non-toxic but flammable gas (b.p. -161degreeC).") +AnnotationAssertion( "CHEBI:16183") +AnnotationAssertion(rdfs:label "methane") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (urea) + +AnnotationAssertion( "A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).") +AnnotationAssertion( "CHEBI:16199") +AnnotationAssertion(rdfs:label "urea") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pyridine) + +AnnotationAssertion( "An azaarene comprising a benzene core in which one -CH group is replaced by a nitrogen atom. It is the parent compound of the class pyridines.") +AnnotationAssertion( "CHEBI:16227") +AnnotationAssertion(rdfs:label "pyridine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydroxide) + +AnnotationAssertion( "CHEBI:16234") +AnnotationAssertion(rdfs:label "hydroxide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleoside 5'-triphosphate) + +AnnotationAssertion( "CHEBI:16381") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleoside 5'-triphosphate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein polypeptide chain) + +AnnotationAssertion( "A naturally occurring polypeptide synthesized at the ribosome.") +AnnotationAssertion( "CHEBI:16541") +AnnotationAssertion(rdfs:label "protein polypeptide chain") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate) + +AnnotationAssertion( "Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.") +AnnotationAssertion( "CHEBI:16646") +AnnotationAssertion(rdfs:label "carbohydrate") +SubClassOf( ) + +# Class: (peptide) + +AnnotationAssertion( "Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.") +AnnotationAssertion( "CHEBI:16670") +AnnotationAssertion(rdfs:label "peptide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside 5'-phosphate) + +AnnotationAssertion( "A ribosyl or deoxyribosyl derivative of a pyrimidine or purine base in which C-5 of the ribose ring is mono-, di-, tri- or tetra-phosphorylated.") +AnnotationAssertion( "CHEBI:16701") +AnnotationAssertion(rdfs:label "nucleoside 5'-phosphate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatinine) + +AnnotationAssertion( "A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.") +AnnotationAssertion( "CHEBI:16737") +AnnotationAssertion(rdfs:label "creatinine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (morpholinium) + +AnnotationAssertion( "A secondary ammonium ion that is the conjugate acid of morpholine resulting from the protonation of the NH group. Major microspecies at pH 7.3.") +AnnotationAssertion( "CHEBI:167868") +AnnotationAssertion(rdfs:label "morpholinium") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatine) + +AnnotationAssertion( "A glycine derivative having methyl and amidino groups attached to the nitrogen.") +AnnotationAssertion( "CHEBI:16919") +AnnotationAssertion(rdfs:label "creatine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (deoxyribonucleic acid) + +AnnotationAssertion( "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.") +AnnotationAssertion( "CHEBI:16991") +AnnotationAssertion(rdfs:label "deoxyribonucleic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrogensulfite) + +AnnotationAssertion( "CHEBI:17137") +AnnotationAssertion(rdfs:label "hydrogensulfite") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA 5'-phosphate polyanion) + +AnnotationAssertion( "CHEBI:173112") +AnnotationAssertion(rdfs:label "DNA 5'-phosphate polyanion") +SubClassOf( ) + +# Class: (sulfite) + +AnnotationAssertion( "A sulfur oxoanion that is the conjugate base of hydrogen sulfite (H2SO3).") +AnnotationAssertion( "CHEBI:17359") +AnnotationAssertion(rdfs:label "sulfite") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyanide) + +AnnotationAssertion( "A pseudohalide anion that is the conjugate base of hydrogen cyanide.") +AnnotationAssertion( "CHEBI:17514") +AnnotationAssertion(rdfs:label "cyanide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrogencarbonate) + +AnnotationAssertion( "The carbon oxoanion resulting from the removal of a proton from carbonic acid.") +AnnotationAssertion( "CHEBI:17544") +AnnotationAssertion(rdfs:label "hydrogencarbonate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrate) + +AnnotationAssertion( "A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3.") +AnnotationAssertion( "CHEBI:17632") +AnnotationAssertion(rdfs:label "nitrate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (geroprotector) + +AnnotationAssertion( "Any compound that supports healthy aging, slows the biological aging process, or extends lifespan.") +AnnotationAssertion( "CHEBI:176497") +AnnotationAssertion(rdfs:label "geroprotector") +SubClassOf( ) + +# Class: (vitamin B7) + +AnnotationAssertion( "Any member of a group of vitamers that belong to the chemical structural class called biotins that exhibit biological activity against vitamin B7 deficiency. Vitamin B7 deficiency is very rare in individuals who take a normal balanced diet. Foods rich in biotin are egg yolk, liver, cereals, vegetables (spinach, mushrooms) and rice. Symptoms associated with vitamin B7 deficiency include thinning hair, scaly skin rashes around eyes, nose and mouth, and brittle nails. The vitamers include biotin and its ionized and salt forms.") +AnnotationAssertion( "CHEBI:176841") +AnnotationAssertion(rdfs:label "vitamin B7") +SubClassOf( ) + +# Class: (organohalogen compound) + +AnnotationAssertion( "A compound containing at least one carbon-halogen bond (where X is a halogen atom).") +AnnotationAssertion( "CHEBI:17792") +AnnotationAssertion(rdfs:label "organohalogen compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (transfer RNA) + +AnnotationAssertion( "A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis.") +AnnotationAssertion( "CHEBI:17843") +AnnotationAssertion(rdfs:label "transfer RNA") +EquivalentClasses( ) +SubClassOf( ) + +# Class: (donor) + +AnnotationAssertion( "A molecular entity that can transfer (\"donate\") an electron, a pair of electrons, an atom or a group to another molecular entity.") +AnnotationAssertion( "CHEBI:17891") +AnnotationAssertion(rdfs:label "donor") +SubClassOf( ) + +# Class: (lipid) + +AnnotationAssertion( "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.") +AnnotationAssertion( "CHEBI:18059") +AnnotationAssertion(rdfs:label "lipid") +SubClassOf( ) + +# Class: (nucleobase) + +AnnotationAssertion( "That part of DNA or RNA that may be involved in pairing.") +AnnotationAssertion( "CHEBI:18282") +AnnotationAssertion(rdfs:label "nucleobase") +SubClassOf( ) + +# Class: (alkane) + +AnnotationAssertion( "An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.") +AnnotationAssertion( "CHEBI:18310") +AnnotationAssertion(rdfs:label "alkane") +SubClassOf( ) +SubClassOf( ) + +# Class: (diphosphate(4-)) + +AnnotationAssertion( "CHEBI:18361") +AnnotationAssertion(rdfs:label "diphosphate(4-)") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphate(3-)) + +AnnotationAssertion( "A phosphate ion that is the conjugate base of hydrogenphosphate.") +AnnotationAssertion( "CHEBI:18367") +AnnotationAssertion(rdfs:label "phosphate(3-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrile) + +AnnotationAssertion( "A compound having the structure RC#N; thus a C-substituted derivative of hydrocyanic acid, HC#N. In systematic nomenclature, the suffix nitrile denotes the triply bound #N atom, not the carbon atom attached to it.") +AnnotationAssertion( "CHEBI:18379") +AnnotationAssertion(rdfs:label "nitrile") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrogen cyanide) + +AnnotationAssertion( "A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom") +AnnotationAssertion( "CHEBI:18407") +AnnotationAssertion(rdfs:label "hydrogen cyanide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleotide) + +AnnotationAssertion( "CHEBI:19260") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleotide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (2-deoxyribose phosphate) + +AnnotationAssertion( "A deoxyaldopentose phosphate in which the deoxyaldopentose is 2-deoxyribose.") +AnnotationAssertion( "CHEBI:19569") +AnnotationAssertion(rdfs:label "2-deoxyribose phosphate") +SubClassOf( ) + +# Class: (NMR solvent) + +AnnotationAssertion( "A solvent used in nuclear magnetic resonance (NMR) spectroscopy.") +AnnotationAssertion( "CHEBI:197449") +AnnotationAssertion(rdfs:label "NMR solvent") +SubClassOf( ) + +# Class: (N-glycosyl compound) + +AnnotationAssertion( "A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.") +AnnotationAssertion( "CHEBI:21731") +AnnotationAssertion(rdfs:label "N-glycosyl compound") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (acyl group) + +AnnotationAssertion( "An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.") +AnnotationAssertion( "CHEBI:22221") +AnnotationAssertion(rdfs:label "acyl group") +SubClassOf( ) + +# Class: (alkali metal atom) + +AnnotationAssertion( "CHEBI:22314") +AnnotationAssertion(rdfs:label "alkali metal atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (anion) + +AnnotationAssertion( "A monoatomic or polyatomic species having one or more elementary charges of the electron.") +AnnotationAssertion( "CHEBI:22563") +AnnotationAssertion(rdfs:label "anion") +SubClassOf( ) + +# Class: (base) + +AnnotationAssertion( "A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).") +AnnotationAssertion( "CHEBI:22695") +AnnotationAssertion(rdfs:label "base") +SubClassOf( ) + +# Class: (benzenes) + +AnnotationAssertion( "Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.") +AnnotationAssertion( "CHEBI:22712") +AnnotationAssertion(rdfs:label "benzenes") +SubClassOf( ) + +# Class: (NMR chemical shift reference compound) + +AnnotationAssertion( "Any compound that produces a peak used as reference frequency in the delta chemical shift scale.") +AnnotationAssertion( "CHEBI:228364") +AnnotationAssertion(rdfs:label "NMR chemical shift reference compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (carbamoyl group) + +AnnotationAssertion( "The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.") +AnnotationAssertion( "CHEBI:23004") +AnnotationAssertion(rdfs:label "carbamoyl group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbonyl group) + +AnnotationAssertion( "CHEBI:23019") +AnnotationAssertion(rdfs:label "carbonyl group") +SubClassOf( ) + +# Class: (chlorine atom) + +AnnotationAssertion( "CHEBI:23116") +AnnotationAssertion(rdfs:label "chlorine atom") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chlorine molecular entity) + +AnnotationAssertion( "A halogen molecular entity containing one or more atoms of chlorine.") +AnnotationAssertion( "CHEBI:23117") +AnnotationAssertion(rdfs:label "chlorine molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroalkane) + +AnnotationAssertion( "Any haloalkane that consists of an alkane substituted by at least one chloro group.") +AnnotationAssertion( "CHEBI:23128") +AnnotationAssertion(rdfs:label "chloroalkane") +SubClassOf( ) +SubClassOf( ) + +# Class: (chlorobenzenes) + +AnnotationAssertion( "Any organochlorine compound containing a benzene ring which is substituted by one or more chlorines.") +AnnotationAssertion( "CHEBI:23132") +AnnotationAssertion(rdfs:label "chlorobenzenes") +SubClassOf( ) +SubClassOf( ) + +# Class: (chloromethanes) + +AnnotationAssertion( "A halomethane that is methane in which one or more hydrogens has been replaced by chlorine.") +AnnotationAssertion( "CHEBI:23148") +AnnotationAssertion(rdfs:label "chloromethanes") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (coenzyme) + +AnnotationAssertion( "A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons.") +AnnotationAssertion( "CHEBI:23354") +AnnotationAssertion(rdfs:label "coenzyme") +SubClassOf( ) + +# Class: (cofactor) + +AnnotationAssertion( "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).") +AnnotationAssertion( "CHEBI:23357") +AnnotationAssertion(rdfs:label "cofactor") +SubClassOf( ) + +# Class: (molecular entity) + +AnnotationAssertion( "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.") +AnnotationAssertion( "We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well"@en) +AnnotationAssertion( "CHEBI:23367") +AnnotationAssertion(rdfs:label "molecular entity") +SubClassOf( ) + +# Class: (cyanides) + +AnnotationAssertion( "Salts and C-organyl derivatives of hydrogen cyanide, HC#N.") +AnnotationAssertion( "CHEBI:23424") +AnnotationAssertion(rdfs:label "cyanides") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyclic amide) + +AnnotationAssertion( "CHEBI:23443") +AnnotationAssertion(rdfs:label "cyclic amide") +SubClassOf( ) + +# Class: (deoxyaldopentose phosphate) + +AnnotationAssertion( "CHEBI:23634") +AnnotationAssertion(rdfs:label "deoxyaldopentose phosphate") +SubClassOf( ) + +# Class: (drug) + +AnnotationAssertion( "Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.") +AnnotationAssertion( "CHEBI:23888") +AnnotationAssertion(rdfs:label "drug") +SubClassOf( ) + +# Class: (monoatomic cation) + +AnnotationAssertion( "CHEBI:23906") +AnnotationAssertion(rdfs:label "monoatomic cation") +SubClassOf( ) +SubClassOf( ) + +# Class: (enzyme inhibitor) + +AnnotationAssertion( "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.") +AnnotationAssertion( "CHEBI:23924") +AnnotationAssertion(rdfs:label "enzyme inhibitor") +SubClassOf( ) +SubClassOf( ) + +# Class: (fungicide) + +AnnotationAssertion( "A substance used to destroy fungal pests.") +AnnotationAssertion( "CHEBI:24127") +AnnotationAssertion(rdfs:label "fungicide") +SubClassOf( ) +SubClassOf( ) + +# Class: (glycine derivative) + +AnnotationAssertion( "A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.") +AnnotationAssertion( "CHEBI:24373") +AnnotationAssertion(rdfs:label "glycine derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chemical entity) + +AnnotationAssertion( "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.") +AnnotationAssertion( "CHEBI:24431") +AnnotationAssertion(rdfs:label "chemical entity") +SubClassOf( ) + +# Class: (biological role) + +AnnotationAssertion( "A role played by the molecular entity or part thereof within a biological context.") +AnnotationAssertion( "CHEBI:24432") +AnnotationAssertion(rdfs:label "biological role") +SubClassOf( ) + +# Class: (group) + +AnnotationAssertion( "A defined linked collection of atoms or a single atom within a molecular entity.") +AnnotationAssertion( "CHEBI:24433") +AnnotationAssertion(rdfs:label "group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (guanidines) + +AnnotationAssertion( "Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas.") +AnnotationAssertion( "CHEBI:24436") +AnnotationAssertion(rdfs:label "guanidines") +SubClassOf( ) + +# Class: (haloalkane) + +AnnotationAssertion( "A halohydrocarbon that is an alkane in which at least one hydrogen atom has been replaced by with a halogen atom.") +AnnotationAssertion( "CHEBI:24469") +AnnotationAssertion(rdfs:label "haloalkane") +SubClassOf( ) + +# Class: (halogen molecular entity) + +AnnotationAssertion( "CHEBI:24471") +AnnotationAssertion(rdfs:label "halogen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (halohydrocarbon) + +AnnotationAssertion( "A compound derived from a hydrocarbon by replacing a hydrogen atom with a halogen atom.") +AnnotationAssertion( "CHEBI:24472") +AnnotationAssertion(rdfs:label "halohydrocarbon") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (halogen) + +AnnotationAssertion( "CHEBI:24473") +AnnotationAssertion(rdfs:label "halogen") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic heterocyclic compound) + +AnnotationAssertion( "A cyclic compound having as ring members atoms of carbon and at least of one other element.") +AnnotationAssertion( "CHEBI:24532") +AnnotationAssertion(rdfs:label "organic heterocyclic compound") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (hydrocarbon) + +AnnotationAssertion( "A compound consisting of carbon and hydrogen only.") +AnnotationAssertion( "CHEBI:24632") +AnnotationAssertion(rdfs:label "hydrocarbon") +SubClassOf( ) + +# Class: (hydroxides) + +AnnotationAssertion( "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).") +AnnotationAssertion( "CHEBI:24651") +AnnotationAssertion(rdfs:label "hydroxides") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxoacid) + +AnnotationAssertion( "A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).") +AnnotationAssertion( "CHEBI:24833") +AnnotationAssertion(rdfs:label "oxoacid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (inorganic anion) + +AnnotationAssertion( "CHEBI:24834") +AnnotationAssertion(rdfs:label "inorganic anion") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic molecular entity) + +AnnotationAssertion( "A molecular entity that contains no carbon.") +AnnotationAssertion( "CHEBI:24835") +AnnotationAssertion(rdfs:label "inorganic molecular entity") +SubClassOf( ) + +# Class: (inorganic oxide) + +AnnotationAssertion( "CHEBI:24836") +AnnotationAssertion(rdfs:label "inorganic oxide") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic salt) + +AnnotationAssertion( "CHEBI:24839") +AnnotationAssertion(rdfs:label "inorganic salt") +SubClassOf( ) +SubClassOf( ) + +# Class: (salt) + +AnnotationAssertion( "A salt is an assembly of cations and anions.") +AnnotationAssertion( "CHEBI:24866") +AnnotationAssertion(rdfs:label "salt") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monoatomic ion) + +AnnotationAssertion( "CHEBI:24867") +AnnotationAssertion(rdfs:label "monoatomic ion") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic salt) + +AnnotationAssertion( "CHEBI:24868") +AnnotationAssertion(rdfs:label "organic salt") +SubClassOf( ) + +# Class: (ion) + +AnnotationAssertion( "A molecular entity having a net electric charge.") +AnnotationAssertion( "CHEBI:24870") +AnnotationAssertion(rdfs:label "ion") +SubClassOf( ) + +# Class: (isoprenoid) + +AnnotationAssertion( "Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives.") +AnnotationAssertion( "CHEBI:24913") +AnnotationAssertion(rdfs:label "isoprenoid") +SubClassOf( ) +SubClassOf( ) + +# Class: (lactam) + +AnnotationAssertion( "Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.") +AnnotationAssertion( "CHEBI:24995") +AnnotationAssertion(rdfs:label "lactam") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (metabolite) + +AnnotationAssertion( "Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.") +AnnotationAssertion( "CHEBI:25212") +AnnotationAssertion(rdfs:label "metabolite") +SubClassOf( ) + +# Class: (metal cation) + +AnnotationAssertion( "CHEBI:25213") +AnnotationAssertion(rdfs:label "metal cation") +SubClassOf( ) +SubClassOf( ) + +# Class: (mitochondrial respiratory-chain inhibitor) + +AnnotationAssertion( "CHEBI:25355") +AnnotationAssertion(rdfs:label "mitochondrial respiratory-chain inhibitor") +SubClassOf( ) + +# Class: (molecule) + +AnnotationAssertion( "Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.") +AnnotationAssertion( "CHEBI:25367") +AnnotationAssertion(rdfs:label "molecule") +SubClassOf( ) + +# Class: (monocarboxylic acid) + +AnnotationAssertion( "An oxoacid containing a single carboxy group.") +AnnotationAssertion( "CHEBI:25384") +AnnotationAssertion(rdfs:label "monocarboxylic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monoatomic monocation) + +AnnotationAssertion( "CHEBI:25414") +AnnotationAssertion(rdfs:label "monoatomic monocation") +SubClassOf( ) + +# Class: (neurotransmitter) + +AnnotationAssertion( "An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.") +AnnotationAssertion( "CHEBI:25512") +AnnotationAssertion(rdfs:label "neurotransmitter") +SubClassOf( ) + +# Class: (nitrogen atom) + +AnnotationAssertion( "CHEBI:25555") +AnnotationAssertion(rdfs:label "nitrogen atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nonmetal atom) + +AnnotationAssertion( "CHEBI:25585") +AnnotationAssertion(rdfs:label "nonmetal atom") +SubClassOf( ) + +# Class: (nucleoside phosphate) + +AnnotationAssertion( "A nucleobase-containing molecular entity that is a nucleoside in which one or more of the sugar hydroxy groups has been converted into a mono- or poly-phosphate. The term includes both nucleotides and non-nucleotide nucleoside phosphates.") +AnnotationAssertion( "CHEBI:25608") +AnnotationAssertion(rdfs:label "nucleoside phosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic heteromonocyclic compound) + +AnnotationAssertion( "CHEBI:25693") +AnnotationAssertion(rdfs:label "organic heteromonocyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic anion) + +AnnotationAssertion( "Any organic ion with a net negative charge.") +AnnotationAssertion( "CHEBI:25696") +AnnotationAssertion(rdfs:label "organic anion") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic cation) + +AnnotationAssertion( "Any organic ion with a net positive charge.") +AnnotationAssertion( "CHEBI:25697") +AnnotationAssertion(rdfs:label "organic cation") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic ion) + +AnnotationAssertion( "CHEBI:25699") +AnnotationAssertion(rdfs:label "organic ion") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic phosphate) + +AnnotationAssertion( "CHEBI:25703") +AnnotationAssertion(rdfs:label "organic phosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (organophosphorus compound) + +AnnotationAssertion( "An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters.") +AnnotationAssertion( "CHEBI:25710") +AnnotationAssertion(rdfs:label "organophosphorus compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (oxide) + +AnnotationAssertion( "An oxide is a chemical compound of oxygen with other chemical elements.") +AnnotationAssertion( "CHEBI:25741") +AnnotationAssertion(rdfs:label "oxide") +SubClassOf( ) +SubClassOf( ) + +# Class: (oxime) + +AnnotationAssertion( "Compounds of structure R2C=NOH derived from condensation of aldehydes or ketones with hydroxylamine. Oximes from aldehydes may be called aldoximes; those from ketones may be called ketoximes.") +AnnotationAssertion( "CHEBI:25750") +AnnotationAssertion(rdfs:label "oxime") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxygen atom) + +AnnotationAssertion( "CHEBI:25805") +AnnotationAssertion(rdfs:label "oxygen atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxygen molecular entity) + +AnnotationAssertion( "CHEBI:25806") +AnnotationAssertion(rdfs:label "oxygen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (aldopentose phosphate) + +AnnotationAssertion( "CHEBI:25900") +AnnotationAssertion(rdfs:label "aldopentose phosphate") +SubClassOf( ) +SubClassOf( ) + +# Class: (pentose) + +AnnotationAssertion( "A five-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldopentose) or a ketone group at position 2 (ketopentose).") +AnnotationAssertion( "CHEBI:25901") +AnnotationAssertion(rdfs:label "pentose") +SubClassOf( ) + +# Class: (pesticide) + +AnnotationAssertion( "Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.") +AnnotationAssertion( "CHEBI:25944") +AnnotationAssertion(rdfs:label "pesticide") +SubClassOf( ) + +# Class: (phosphate) + +AnnotationAssertion( "Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.") +AnnotationAssertion( "CHEBI:26020") +AnnotationAssertion(rdfs:label "phosphate") +SubClassOf( ) + +# Class: (phosphoric acid) + +AnnotationAssertion( "A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.") +AnnotationAssertion( "CHEBI:26078") +AnnotationAssertion(rdfs:label "phosphoric acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphoric acid derivative) + +AnnotationAssertion( "CHEBI:26079") +AnnotationAssertion(rdfs:label "phosphoric acid derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus molecular entity) + +AnnotationAssertion( "CHEBI:26082") +AnnotationAssertion(rdfs:label "phosphorus molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (prosthetic group) + +AnnotationAssertion( "A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity.") +AnnotationAssertion( "CHEBI:26348") +AnnotationAssertion(rdfs:label "prosthetic group") +SubClassOf( ) + +# Class: (pyridines) + +AnnotationAssertion( "Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives.") +AnnotationAssertion( "CHEBI:26421") +AnnotationAssertion(rdfs:label "pyridines") +SubClassOf( ) +SubClassOf( ) + +# Class: (serine family amino acid) + +AnnotationAssertion( "An alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class.") +AnnotationAssertion( "CHEBI:26650") +AnnotationAssertion(rdfs:label "serine family amino acid") +SubClassOf( ) + +# Class: (sodium atom) + +AnnotationAssertion( "CHEBI:26708") +AnnotationAssertion(rdfs:label "sodium atom") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sodium molecular entity) + +AnnotationAssertion( "CHEBI:26712") +AnnotationAssertion(rdfs:label "sodium molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sodium salt) + +AnnotationAssertion( "Any alkali metal salt having sodium(1+) as the cation.") +AnnotationAssertion( "CHEBI:26714") +AnnotationAssertion(rdfs:label "sodium salt") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate phosphate) + +AnnotationAssertion( "CHEBI:26816") +AnnotationAssertion(rdfs:label "carbohydrate phosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (sulfur atom) + +AnnotationAssertion( "CHEBI:26833") +AnnotationAssertion(rdfs:label "sulfur atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sulfur molecular entity) + +AnnotationAssertion( "CHEBI:26835") +AnnotationAssertion(rdfs:label "sulfur molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxolanes) + +AnnotationAssertion( "Any oxacycle having an oxolane (tetrahydrofuran) skeleton.") +AnnotationAssertion( "CHEBI:26912") +AnnotationAssertion(rdfs:label "oxolanes") +SubClassOf( ) +SubClassOf( ) + +# Class: (micronutrient) + +AnnotationAssertion( "Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.") +AnnotationAssertion( "CHEBI:27027") +AnnotationAssertion(rdfs:label "micronutrient") +SubClassOf( ) + +# Class: (organic heterobicyclic compound) + +AnnotationAssertion( "CHEBI:27171") +AnnotationAssertion(rdfs:label "organic heterobicyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (univalent carboacyl group) + +AnnotationAssertion( "A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.") +AnnotationAssertion( "CHEBI:27207") +AnnotationAssertion(rdfs:label "univalent carboacyl group") +SubClassOf( ) + +# Class: (water-soluble vitamin (role)) + +AnnotationAssertion( "Any vitamin that dissolves in water and readily absorbed into tissues for immediate use. Unlike the fat-soluble vitamins, they are not stored in the body and need to be replenished regularly in the diet and will rarely accumulate to toxic levels since they are quickly excreted from the body via urine.") +AnnotationAssertion( "CHEBI:27314") +AnnotationAssertion(rdfs:label "water-soluble vitamin (role)") +SubClassOf( ) + +# Class: (zwitterion) + +AnnotationAssertion( "A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).") +AnnotationAssertion( "CHEBI:27369") +AnnotationAssertion(rdfs:label "zwitterion") +SubClassOf( ) + +# Class: (carbon atom) + +AnnotationAssertion( "CHEBI:27594") +AnnotationAssertion(rdfs:label "carbon atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbamic acid) + +AnnotationAssertion( "A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.") +AnnotationAssertion( "CHEBI:28616") +AnnotationAssertion(rdfs:label "carbamic acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus atom) + +AnnotationAssertion( "CHEBI:28659") +AnnotationAssertion(rdfs:label "phosphorus atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ammonium) + +AnnotationAssertion( "An onium cation obtained by protonation of ammonia.") +AnnotationAssertion( "CHEBI:28938") +AnnotationAssertion(rdfs:label "ammonium") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbonic acid) + +AnnotationAssertion( "CHEBI:28976") +AnnotationAssertion(rdfs:label "carbonic acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carboxylic acid anion) + +AnnotationAssertion( "The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.") +AnnotationAssertion( "CHEBI:29067") +AnnotationAssertion(rdfs:label "carboxylic acid anion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mononucleotide) + +AnnotationAssertion( "CHEBI:29075") +AnnotationAssertion(rdfs:label "mononucleotide") +SubClassOf( ) + +# Class: (sodium(1+)) + +AnnotationAssertion( "A monoatomic monocation obtained from sodium.") +AnnotationAssertion( "CHEBI:29101") +AnnotationAssertion(rdfs:label "sodium(1+)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sulfonic acid) + +AnnotationAssertion( "CHEBI:29214") +AnnotationAssertion(rdfs:label "sulfonic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (azanide) + +AnnotationAssertion( "CHEBI:29337") +AnnotationAssertion(rdfs:label "azanide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydridonitrate(2-)) + +AnnotationAssertion( "A divalent inorganic anion resulting from the removal of two protons from ammonia.") +AnnotationAssertion( "CHEBI:29340") +AnnotationAssertion(rdfs:label "hydridonitrate(2-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monocarboxylic acid amide) + +AnnotationAssertion( "A carboxamide derived from a monocarboxylic acid.") +AnnotationAssertion( "CHEBI:29347") +AnnotationAssertion(rdfs:label "monocarboxylic acid amide") +SubClassOf( ) + +# Class: (methanediide) + +AnnotationAssertion( "CHEBI:29360") +AnnotationAssertion(rdfs:label "methanediide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxonium) + +AnnotationAssertion( "CHEBI:29412") +AnnotationAssertion(rdfs:label "oxonium") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (methanide) + +AnnotationAssertion( "CHEBI:29438") +AnnotationAssertion(rdfs:label "methanide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitro group) + +AnnotationAssertion( "CHEBI:29785") +AnnotationAssertion(rdfs:label "nitro group") +SubClassOf( ) +SubClassOf( ) + +# Class: (diphosphoric acid) + +AnnotationAssertion( "An acyclic phosphorus acid anhydride obtained by condensation of two molecules of phosphoric acid.") +AnnotationAssertion( "CHEBI:29888") +AnnotationAssertion(rdfs:label "diphosphoric acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (acetate) + +AnnotationAssertion( "A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid.") +AnnotationAssertion( "CHEBI:30089") +AnnotationAssertion(rdfs:label "acetate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycinium) + +AnnotationAssertion( "An alpha-amino-acid cation that is the conjugate acid of glycine, arising from protonation of the amino.") +AnnotationAssertion( "CHEBI:32507") +AnnotationAssertion(rdfs:label "glycinium") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycinate) + +AnnotationAssertion( "An alpha-amino-acid anion that is the conjugate base of glycine, arising from deprotonation of the carboxy group.") +AnnotationAssertion( "CHEBI:32508") +AnnotationAssertion(rdfs:label "glycinate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (secondary amine) + +AnnotationAssertion( "A compound formally derived from ammonia by replacing two hydrogen atoms by hydrocarbyl groups.") +AnnotationAssertion( "CHEBI:32863") +AnnotationAssertion(rdfs:label "secondary amine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amine) + +AnnotationAssertion( "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.") +AnnotationAssertion( "CHEBI:32952") +AnnotationAssertion(rdfs:label "amine") +SubClassOf( ) + +# Class: (sodium acetate) + +AnnotationAssertion( "CHEBI:32954") +AnnotationAssertion(rdfs:label "sodium acetate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amide) + +AnnotationAssertion( "An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.") +AnnotationAssertion( "CHEBI:32988") +AnnotationAssertion(rdfs:label "amide") +SubClassOf( ) + +# Class: (diphosphate(1-)) + +AnnotationAssertion( "A monovalent inorganic anion obtained by deprotonation of one of the phosphate OH groups in diphosphoric acid.") +AnnotationAssertion( "CHEBI:33017") +AnnotationAssertion(rdfs:label "diphosphate(1-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (diphosphate(3-)) + +AnnotationAssertion( "A trivalent inorganic anion obtained by removal of all three protons from diphosphoric acid.") +AnnotationAssertion( "CHEBI:33019") +AnnotationAssertion(rdfs:label "diphosphate(3-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vitamin (role)) + +AnnotationAssertion( "A biochemical role played by any micronutrient that is an organic compound. Vitamins are present in foods in small amounts and are essential to normal metabolism and biochemical functions, usually as coenzymes. The term \"vitamines\" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines.") +AnnotationAssertion( "CHEBI:33229") +AnnotationAssertion(rdfs:label "vitamin (role)") +SubClassOf( ) +SubClassOf( ) + +# Class: (application) + +AnnotationAssertion( "Intended use of the molecular entity or part thereof by humans.") +AnnotationAssertion( "CHEBI:33232") +AnnotationAssertion(rdfs:label "application") +SubClassOf( ) + +# Class: (fundamental particle) + +AnnotationAssertion( "A particle not known to have substructure.") +AnnotationAssertion( "CHEBI:33233") +AnnotationAssertion(rdfs:label "fundamental particle") +SubClassOf( ) + +# Class: (monoatomic entity) + +AnnotationAssertion( "A monoatomic entity is a molecular entity consisting of a single atom.") +AnnotationAssertion( "CHEBI:33238") +AnnotationAssertion(rdfs:label "monoatomic entity") +SubClassOf( ) + +# Class: (oxoacid derivative) + +AnnotationAssertion( "CHEBI:33241") +AnnotationAssertion(rdfs:label "oxoacid derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (inorganic hydride) + +AnnotationAssertion( "CHEBI:33242") +AnnotationAssertion(rdfs:label "inorganic hydride") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic fundamental parent) + +AnnotationAssertion( "An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.") +AnnotationAssertion( "CHEBI:33245") +AnnotationAssertion(rdfs:label "organic fundamental parent") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic group) + +AnnotationAssertion( "Any substituent group which does not contain carbon.") +AnnotationAssertion( "CHEBI:33246") +AnnotationAssertion(rdfs:label "inorganic group") +SubClassOf( ) + +# Class: (organic group) + +AnnotationAssertion( "Any substituent group or skeleton containing carbon.") +AnnotationAssertion( "CHEBI:33247") +AnnotationAssertion(rdfs:label "organic group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organyl group) + +AnnotationAssertion( "Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.") +AnnotationAssertion( "CHEBI:33249") +AnnotationAssertion(rdfs:label "organyl group") +SubClassOf( ) + +# Class: (atom) + +AnnotationAssertion( "A chemical entity constituting the smallest component of an element having the chemical properties of the element.") +AnnotationAssertion( "CHEBI:33250") +AnnotationAssertion(rdfs:label "atom") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (atomic nucleus) + +AnnotationAssertion( "A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.") +AnnotationAssertion( "CHEBI:33252") +AnnotationAssertion(rdfs:label "atomic nucleus") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleon) + +AnnotationAssertion( "Heavy nuclear particle: proton or neutron.") +AnnotationAssertion( "CHEBI:33253") +AnnotationAssertion(rdfs:label "nucleon") +SubClassOf( ) +SubClassOf( ) + +# Class: (primary amide) + +AnnotationAssertion( "A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.") +AnnotationAssertion( "CHEBI:33256") +AnnotationAssertion(rdfs:label "primary amide") +SubClassOf( ) + +# Class: (elemental molecular entity) + +AnnotationAssertion( "A molecular entity all atoms of which have the same atomic number.") +AnnotationAssertion( "CHEBI:33259") +AnnotationAssertion(rdfs:label "elemental molecular entity") +SubClassOf( ) + +# Class: (organosulfur compound) + +AnnotationAssertion( "An organosulfur compound is a compound containing at least one carbon-sulfur bond.") +AnnotationAssertion( "CHEBI:33261") +AnnotationAssertion(rdfs:label "organosulfur compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (polyatomic anion) + +AnnotationAssertion( "An anion consisting of more than one atom.") +AnnotationAssertion( "CHEBI:33273") +AnnotationAssertion(rdfs:label "polyatomic anion") +SubClassOf( ) +SubClassOf( ) + +# Class: (molecular messenger) + +AnnotationAssertion( "CHEBI:33280") +AnnotationAssertion(rdfs:label "molecular messenger") +SubClassOf( ) + +# Class: (antimicrobial agent) + +AnnotationAssertion( "A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.") +AnnotationAssertion( "CHEBI:33281") +AnnotationAssertion(rdfs:label "antimicrobial agent") +SubClassOf( ) + +# Class: (nutrient) + +AnnotationAssertion( "A nutrient is a food component that an organism uses to survive and grow.") +AnnotationAssertion( "CHEBI:33284") +AnnotationAssertion(rdfs:label "nutrient") +SubClassOf( ) + +# Class: (heteroorganic entity) + +AnnotationAssertion( "A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.") +AnnotationAssertion( "CHEBI:33285") +AnnotationAssertion(rdfs:label "heteroorganic entity") +SubClassOf( ) + +# Class: (agrochemical) + +AnnotationAssertion( "An agrochemical is a substance that is used in agriculture or horticulture.") +AnnotationAssertion( "CHEBI:33286") +AnnotationAssertion(rdfs:label "agrochemical") +SubClassOf( ) + +# Class: (fertilizer) + +AnnotationAssertion( "A fertilizer is any substance that is added to soil or water to assist the growth of plants.") +AnnotationAssertion( "CHEBI:33287") +AnnotationAssertion(rdfs:label "fertilizer") +SubClassOf( ) + +# Class: (fuel) + +AnnotationAssertion( "An energy-rich substance that can be transformed with release of usable energy.") +AnnotationAssertion( "CHEBI:33292") +AnnotationAssertion(rdfs:label "fuel") +SubClassOf( ) + +# Class: (diagnostic agent) + +AnnotationAssertion( "A substance administered to aid diagnosis of a disease.") +AnnotationAssertion( "CHEBI:33295") +AnnotationAssertion(rdfs:label "diagnostic agent") +SubClassOf( ) + +# Class: (alkali metal molecular entity) + +AnnotationAssertion( "A molecular entity containing one or more atoms of an alkali metal.") +AnnotationAssertion( "CHEBI:33296") +AnnotationAssertion(rdfs:label "alkali metal molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pnictogen) + +AnnotationAssertion( "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.") +AnnotationAssertion( "CHEBI:33300") +AnnotationAssertion(rdfs:label "pnictogen") +SubClassOf( ) + +# Class: (pnictogen molecular entity) + +AnnotationAssertion( "A p-block molecular entity containing any pnictogen.") +AnnotationAssertion( "CHEBI:33302") +AnnotationAssertion(rdfs:label "pnictogen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chalcogen) + +AnnotationAssertion( "Any p-block element belonging to the group 16 family of the periodic table.") +AnnotationAssertion( "CHEBI:33303") +AnnotationAssertion(rdfs:label "chalcogen") +SubClassOf( ) + +# Class: (chalcogen molecular entity) + +AnnotationAssertion( "Any p-block molecular entity containing a chalcogen.") +AnnotationAssertion( "CHEBI:33304") +AnnotationAssertion(rdfs:label "chalcogen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbon group element atom) + +AnnotationAssertion( "CHEBI:33306") +AnnotationAssertion(rdfs:label "carbon group element atom") +SubClassOf( ) + +# Class: (main group element atom) + +AnnotationAssertion( "An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.") +AnnotationAssertion( "CHEBI:33318") +AnnotationAssertion(rdfs:label "main group element atom") +SubClassOf( ) + +# Class: (sulfur oxoacid) + +AnnotationAssertion( "CHEBI:33402") +AnnotationAssertion(rdfs:label "sulfur oxoacid") +SubClassOf( ) +SubClassOf( ) + +# Class: (hydracid) + +AnnotationAssertion( "A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).") +AnnotationAssertion( "CHEBI:33405") +AnnotationAssertion(rdfs:label "hydracid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pnictogen oxoacid) + +AnnotationAssertion( "CHEBI:33408") +AnnotationAssertion(rdfs:label "pnictogen oxoacid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phospho sugar) + +AnnotationAssertion( "Any monosaccharide containing an alcoholic hydroxy group esterified with phosphoric acid.") +AnnotationAssertion( "CHEBI:33447") +AnnotationAssertion(rdfs:label "phospho sugar") +SubClassOf( ) +SubClassOf( ) + +# Class: (nitrogen oxoacid) + +AnnotationAssertion( "CHEBI:33455") +AnnotationAssertion(rdfs:label "nitrogen oxoacid") +SubClassOf( ) +SubClassOf( ) + +# Class: (phosphorus oxoacid) + +AnnotationAssertion( "A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.") +AnnotationAssertion( "CHEBI:33457") +AnnotationAssertion(rdfs:label "phosphorus oxoacid") +SubClassOf( ) +SubClassOf( ) + +# Class: (nitrogen oxoanion) + +AnnotationAssertion( "CHEBI:33458") +AnnotationAssertion(rdfs:label "nitrogen oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (pnictogen oxoanion) + +AnnotationAssertion( "CHEBI:33459") +AnnotationAssertion(rdfs:label "pnictogen oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (phosphorus oxoanion) + +AnnotationAssertion( "CHEBI:33461") +AnnotationAssertion(rdfs:label "phosphorus oxoanion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (sulfur oxoanion) + +AnnotationAssertion( "CHEBI:33482") +AnnotationAssertion(rdfs:label "sulfur oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (chalcogen oxoacid) + +AnnotationAssertion( "CHEBI:33484") +AnnotationAssertion(rdfs:label "chalcogen oxoacid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chalcogen oxoanion) + +AnnotationAssertion( "CHEBI:33485") +AnnotationAssertion(rdfs:label "chalcogen oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (alkali metal cation) + +AnnotationAssertion( "CHEBI:33504") +AnnotationAssertion(rdfs:label "alkali metal cation") +SubClassOf( ) + +# Class: (metal atom) + +AnnotationAssertion( "An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.") +AnnotationAssertion( "CHEBI:33521") +AnnotationAssertion(rdfs:label "metal atom") +SubClassOf( ) + +# Class: (sulfonate) + +AnnotationAssertion( "The sulfur oxoanion formed by deprotonation of sulfonic acid.") +AnnotationAssertion( "CHEBI:33543") +AnnotationAssertion(rdfs:label "sulfonate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino-acid anion) + +AnnotationAssertion( "An amino-acid anion obtained by deprotonation of any alpha-amino acid.") +AnnotationAssertion( "CHEBI:33558") +AnnotationAssertion(rdfs:label "alpha-amino-acid anion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (s-block element atom) + +AnnotationAssertion( "CHEBI:33559") +AnnotationAssertion(rdfs:label "s-block element atom") +SubClassOf( ) + +# Class: (p-block element atom) + +AnnotationAssertion( "Any main group element atom belonging to the p-block of the periodic table.") +AnnotationAssertion( "CHEBI:33560") +AnnotationAssertion(rdfs:label "p-block element atom") +SubClassOf( ) + +# Class: (carboxylic acid) + +AnnotationAssertion( "A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.") +AnnotationAssertion( "CHEBI:33575") +AnnotationAssertion(rdfs:label "carboxylic acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (main group molecular entity) + +AnnotationAssertion( "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.") +AnnotationAssertion( "CHEBI:33579") +AnnotationAssertion(rdfs:label "main group molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbon group molecular entity) + +AnnotationAssertion( "CHEBI:33582") +AnnotationAssertion(rdfs:label "carbon group molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyclic compound) + +AnnotationAssertion( "Any molecule that consists of a series of atoms joined together to form a ring.") +AnnotationAssertion( "CHEBI:33595") +AnnotationAssertion(rdfs:label "cyclic compound") +SubClassOf( ) + +# Class: (homocyclic compound) + +AnnotationAssertion( "A cyclic compound having as ring members atoms of the same element only.") +AnnotationAssertion( "CHEBI:33597") +AnnotationAssertion(rdfs:label "homocyclic compound") +SubClassOf( ) + +# Class: (carbocyclic compound) + +AnnotationAssertion( "A homocyclic compound in which all of the ring members are carbon atoms.") +AnnotationAssertion( "CHEBI:33598") +AnnotationAssertion(rdfs:label "carbocyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (hydrogen molecular entity) + +AnnotationAssertion( "CHEBI:33608") +AnnotationAssertion(rdfs:label "hydrogen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (polycyclic compound) + +AnnotationAssertion( "CHEBI:33635") +AnnotationAssertion(rdfs:label "polycyclic compound") +SubClassOf( ) + +# Class: (bicyclic compound) + +AnnotationAssertion( "A molecule that features two fused rings.") +AnnotationAssertion( "CHEBI:33636") +AnnotationAssertion(rdfs:label "bicyclic compound") +SubClassOf( ) + +# Class: (aliphatic compound) + +AnnotationAssertion( "Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds.") +AnnotationAssertion( "CHEBI:33653") +AnnotationAssertion(rdfs:label "aliphatic compound") +SubClassOf( ) + +# Class: (aromatic compound) + +AnnotationAssertion( "A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.") +AnnotationAssertion( "CHEBI:33655") +AnnotationAssertion(rdfs:label "aromatic compound") +SubClassOf( ) + +# Class: (organic aromatic compound) + +AnnotationAssertion( "CHEBI:33659") +AnnotationAssertion(rdfs:label "organic aromatic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (monocyclic compound) + +AnnotationAssertion( "CHEBI:33661") +AnnotationAssertion(rdfs:label "monocyclic compound") +SubClassOf( ) + +# Class: (heteromonocyclic compound) + +AnnotationAssertion( "CHEBI:33670") +AnnotationAssertion(rdfs:label "heteromonocyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (heteropolycyclic compound) + +AnnotationAssertion( "A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.") +AnnotationAssertion( "CHEBI:33671") +AnnotationAssertion(rdfs:label "heteropolycyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (heterobicyclic compound) + +AnnotationAssertion( "A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.") +AnnotationAssertion( "CHEBI:33672") +AnnotationAssertion(rdfs:label "heterobicyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (s-block molecular entity) + +AnnotationAssertion( "An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.") +AnnotationAssertion( "CHEBI:33674") +AnnotationAssertion(rdfs:label "s-block molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (p-block molecular entity) + +AnnotationAssertion( "A main group molecular entity that contains one or more atoms of a p-block element.") +AnnotationAssertion( "CHEBI:33675") +AnnotationAssertion(rdfs:label "p-block molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrides) + +AnnotationAssertion( "Hydrides are chemical compounds of hydrogen with other chemical elements.") +AnnotationAssertion( "CHEBI:33692") +AnnotationAssertion(rdfs:label "hydrides") +SubClassOf( ) +SubClassOf( ) + +# Class: (oxygen hydride) + +AnnotationAssertion( "CHEBI:33693") +AnnotationAssertion(rdfs:label "oxygen hydride") +SubClassOf( ) + +# Class: (biomacromolecule) + +AnnotationAssertion( "A macromolecule formed by a living organism.") +AnnotationAssertion( "CHEBI:33694") +AnnotationAssertion(rdfs:label "biomacromolecule") +SubClassOf( ) +SubClassOf( ) + +# Class: (information biomacromolecule) + +AnnotationAssertion( "CHEBI:33695") +AnnotationAssertion(rdfs:label "information biomacromolecule") +SubClassOf( ) + +# Class: (nucleic acid) + +AnnotationAssertion( "A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.") +AnnotationAssertion( "CHEBI:33696") +AnnotationAssertion(rdfs:label "nucleic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ribonucleic acid) + +AnnotationAssertion( "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.") +AnnotationAssertion( "CHEBI:33697") +AnnotationAssertion(rdfs:label "ribonucleic acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (proteinogenic amino-acid residue) + +AnnotationAssertion( "CHEBI:33700") +AnnotationAssertion(rdfs:label "proteinogenic amino-acid residue") +SubClassOf( ) + +# Class: (polyatomic cation) + +AnnotationAssertion( "A cation consisting of more than one atom.") +AnnotationAssertion( "CHEBI:33702") +AnnotationAssertion(rdfs:label "polyatomic cation") +SubClassOf( ) +SubClassOf( ) + +# Class: (amino-acid cation) + +AnnotationAssertion( "CHEBI:33703") +AnnotationAssertion(rdfs:label "amino-acid cation") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino acid) + +AnnotationAssertion( "An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.") +AnnotationAssertion( "CHEBI:33704") +AnnotationAssertion(rdfs:label "alpha-amino acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino-acid residue) + +AnnotationAssertion( "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.") +AnnotationAssertion( "CHEBI:33708") +AnnotationAssertion(rdfs:label "amino-acid residue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid) + +AnnotationAssertion( "A carboxylic acid containing one or more amino groups.") +AnnotationAssertion( "CHEBI:33709") +AnnotationAssertion(rdfs:label "amino acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino-acid residue) + +AnnotationAssertion( "An amino-acid residue derived from an alpha-amino acid.") +AnnotationAssertion( "CHEBI:33710") +AnnotationAssertion(rdfs:label "alpha-amino-acid residue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino-acid cation) + +AnnotationAssertion( "CHEBI:33719") +AnnotationAssertion(rdfs:label "alpha-amino-acid cation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (canonical nucleoside residue) + +AnnotationAssertion( "CHEBI:33791") +AnnotationAssertion(rdfs:label "canonical nucleoside residue") +SubClassOf( ) + +# Class: (canonical ribonucleoside residue) + +AnnotationAssertion( "CHEBI:33792") +AnnotationAssertion(rdfs:label "canonical ribonucleoside residue") +SubClassOf( ) + +# Class: (canonical deoxyribonucleoside residue) + +AnnotationAssertion( "CHEBI:33793") +AnnotationAssertion(rdfs:label "canonical deoxyribonucleoside residue") +SubClassOf( ) + +# Class: (organic cyclic compound) + +AnnotationAssertion( "Any organic molecule that consists of atoms connected in the form of a ring.") +AnnotationAssertion( "CHEBI:33832") +AnnotationAssertion(rdfs:label "organic cyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (heteroarene) + +AnnotationAssertion( "A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).") +AnnotationAssertion( "CHEBI:33833") +AnnotationAssertion(rdfs:label "heteroarene") +SubClassOf( ) +SubClassOf( ) + +# Class: (benzenoid aromatic compound) + +AnnotationAssertion( "CHEBI:33836") +AnnotationAssertion(rdfs:label "benzenoid aromatic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (nucleoside) + +AnnotationAssertion( "An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.") +AnnotationAssertion( "CHEBI:33838") +AnnotationAssertion(rdfs:label "nucleoside") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (macromolecule) + +AnnotationAssertion( "A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") +AnnotationAssertion( "polymer"@en) +AnnotationAssertion( "CHEBI:33839") +AnnotationAssertion(rdfs:label "macromolecule") +SubClassOf( ) + +# Class: (reagent) + +AnnotationAssertion( "A substance used in a chemical reaction to detect, measure, examine, or produce other substances.") +AnnotationAssertion( "CHEBI:33893") +AnnotationAssertion(rdfs:label "reagent") +SubClassOf( ) + +# Class: (macronutrient) + +AnnotationAssertion( "Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.") +AnnotationAssertion( "CHEBI:33937") +AnnotationAssertion(rdfs:label "macronutrient") +SubClassOf( ) + +# Class: (morpholine) + +AnnotationAssertion( "An organic heteromonocyclic compound whose six-membered ring contains four carbon atoms and one nitrogen atom and one oxygen atom that lies opposite to each other; the parent compound of the morpholine family.") +AnnotationAssertion( "CHEBI:34856") +AnnotationAssertion(rdfs:label "morpholine") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrogen hydride) + +AnnotationAssertion( "CHEBI:35106") +AnnotationAssertion(rdfs:label "nitrogen hydride") +SubClassOf( ) +SubClassOf( ) + +# Class: (azane) + +AnnotationAssertion( "Saturated acyclic nitrogen hydrides having the general formula NnHn+2.") +AnnotationAssertion( "CHEBI:35107") +AnnotationAssertion(rdfs:label "azane") +SubClassOf( ) + +# Class: (aldose phosphate) + +AnnotationAssertion( "CHEBI:35131") +AnnotationAssertion(rdfs:label "aldose phosphate") +SubClassOf( ) + +# Class: (inhibitor) + +AnnotationAssertion( "A substance that diminishes the rate of a chemical reaction.") +AnnotationAssertion( "CHEBI:35222") +AnnotationAssertion(rdfs:label "inhibitor") +SubClassOf( ) + +# Class: (fossil fuel) + +AnnotationAssertion( "A fuel such as coal, oil and natural gas which has formed over many years through the decomposition of deposited vegetation which was under extreme pressure of an overburden of earth.") +AnnotationAssertion( "CHEBI:35230") +AnnotationAssertion(rdfs:label "fossil fuel") +SubClassOf( ) + +# Class: (amino-acid zwitterion) + +AnnotationAssertion( "The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.") +AnnotationAssertion( "CHEBI:35238") +AnnotationAssertion(rdfs:label "amino-acid zwitterion") +SubClassOf( ) + +# Class: (chloroform) + +AnnotationAssertion( "A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines.") +AnnotationAssertion( "CHEBI:35255") +AnnotationAssertion(rdfs:label "chloroform") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ammonium ion derivative) + +AnnotationAssertion( "A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc).") +AnnotationAssertion( "CHEBI:35274") +AnnotationAssertion(rdfs:label "ammonium ion derivative") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organonitrogen compound) + +AnnotationAssertion( "Any heteroorganic entity containing at least one carbon-nitrogen bond.") +AnnotationAssertion( "CHEBI:35352") +AnnotationAssertion(rdfs:label "organonitrogen compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (monosaccharide) + +AnnotationAssertion( "Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group.") +AnnotationAssertion( "CHEBI:35381") +AnnotationAssertion(rdfs:label "monosaccharide") +SubClassOf( ) + +# Class: (oxoanion) + +AnnotationAssertion( "An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.") +AnnotationAssertion( "CHEBI:35406") +AnnotationAssertion(rdfs:label "oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (central nervous system drug) + +AnnotationAssertion( "A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.") +AnnotationAssertion( "CHEBI:35470") +AnnotationAssertion(rdfs:label "central nervous system drug") +SubClassOf( ) + +# Class: (alkali metal salt) + +AnnotationAssertion( "CHEBI:35479") +AnnotationAssertion(rdfs:label "alkali metal salt") +SubClassOf( ) +SubClassOf( ) + +# Class: (heterocyclic organic fundamental parent) + +AnnotationAssertion( "CHEBI:35552") +AnnotationAssertion(rdfs:label "heterocyclic organic fundamental parent") +SubClassOf( ) + +# Class: (mancude organic heteromonocyclic parent) + +AnnotationAssertion( "CHEBI:35555") +AnnotationAssertion(rdfs:label "mancude organic heteromonocyclic parent") +SubClassOf( ) +SubClassOf( ) + +# Class: (mancude ring) + +AnnotationAssertion( "Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds.") +AnnotationAssertion( "CHEBI:35568") +AnnotationAssertion(rdfs:label "mancude ring") +SubClassOf( ) + +# Class: (mancude organic heterocyclic parent) + +AnnotationAssertion( "CHEBI:35571") +AnnotationAssertion(rdfs:label "mancude organic heterocyclic parent") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic mancude parent) + +AnnotationAssertion( "CHEBI:35573") +AnnotationAssertion(rdfs:label "organic mancude parent") +SubClassOf( ) +SubClassOf( ) + +# Class: (carbon oxoanion) + +AnnotationAssertion( "A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n.") +AnnotationAssertion( "CHEBI:35604") +AnnotationAssertion(rdfs:label "carbon oxoanion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (carbon oxoacid) + +AnnotationAssertion( "CHEBI:35605") +AnnotationAssertion(rdfs:label "carbon oxoacid") +SubClassOf( ) +SubClassOf( ) + +# Class: (ester) + +AnnotationAssertion( "A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.") +AnnotationAssertion( "CHEBI:35701") +AnnotationAssertion(rdfs:label "ester") +SubClassOf( ) + +# Class: (nitro compound) + +AnnotationAssertion( "A compound having a nitro group, -NO2 (free valence on nitrogen), which may be attached to carbon, nitrogen (as in nitramines), or oxygen (as in nitrates), among other elements (in the absence of specification, C-nitro compounds are usually implied).") +AnnotationAssertion( "CHEBI:35715") +AnnotationAssertion(rdfs:label "nitro compound") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (C-nitro compound) + +AnnotationAssertion( "A nitro compound having the nitro group (-NO2) attached to a carbon atom.") +AnnotationAssertion( "CHEBI:35716") +AnnotationAssertion(rdfs:label "C-nitro compound") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (antifungal agent) + +AnnotationAssertion( "An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce.") +AnnotationAssertion( "CHEBI:35718") +AnnotationAssertion(rdfs:label "antifungal agent") +SubClassOf( ) + +# Class: (monocarboxylic acid anion) + +AnnotationAssertion( "A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.") +AnnotationAssertion( "CHEBI:35757") +AnnotationAssertion(rdfs:label "monocarboxylic acid anion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphate ion) + +AnnotationAssertion( "A phosphorus oxoanion that is the conjugate base of phosphoric acid.") +AnnotationAssertion( "CHEBI:35780") +AnnotationAssertion(rdfs:label "phosphate ion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (diphosphate ion) + +AnnotationAssertion( "CHEBI:35782") +AnnotationAssertion(rdfs:label "diphosphate ion") +SubClassOf( ) + +# Class: (pnictogen hydride) + +AnnotationAssertion( "CHEBI:35881") +AnnotationAssertion(rdfs:label "pnictogen hydride") +SubClassOf( ) +SubClassOf( ) + +# Class: (neurotransmitter agent) + +AnnotationAssertion( "A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function.") +AnnotationAssertion( "CHEBI:35942") +AnnotationAssertion(rdfs:label "neurotransmitter agent") +SubClassOf( ) +SubClassOf( ) + +# Class: (protein) + +AnnotationAssertion( "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.") +AnnotationAssertion( "CHEBI:36080") +AnnotationAssertion(rdfs:label "protein") +EquivalentClasses( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lepton) + +AnnotationAssertion( "Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).") +AnnotationAssertion( "CHEBI:36338") +AnnotationAssertion(rdfs:label "lepton") +SubClassOf( ) +SubClassOf( ) + +# Class: (baryon) + +AnnotationAssertion( "Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).") +AnnotationAssertion( "CHEBI:36339") +AnnotationAssertion(rdfs:label "baryon") +SubClassOf( ) +SubClassOf( ) + +# Class: (fermion) + +AnnotationAssertion( "Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.") +AnnotationAssertion( "CHEBI:36340") +AnnotationAssertion(rdfs:label "fermion") +SubClassOf( ) + +# Class: (subatomic particle) + +AnnotationAssertion( "A particle smaller than an atom.") +AnnotationAssertion( "CHEBI:36342") +AnnotationAssertion(rdfs:label "subatomic particle") + +# Class: (composite particle) + +AnnotationAssertion( "A subatomic particle known to have substructure (i.e. consisting of smaller particles).") +AnnotationAssertion( "CHEBI:36343") +AnnotationAssertion(rdfs:label "composite particle") +SubClassOf( ) + +# Class: (hadron) + +AnnotationAssertion( "Hadron is a subatomic particle which experiences the strong force.") +AnnotationAssertion( "CHEBI:36344") +AnnotationAssertion(rdfs:label "hadron") +SubClassOf( ) + +# Class: (nuclear particle) + +AnnotationAssertion( "A nucleus or any of its constituents in any of their energy states.") +AnnotationAssertion( "CHEBI:36347") +AnnotationAssertion(rdfs:label "nuclear particle") +SubClassOf( ) + +# Class: (polyatomic entity) + +AnnotationAssertion( "Any molecular entity consisting of more than one atom.") +AnnotationAssertion( "CHEBI:36357") +AnnotationAssertion(rdfs:label "polyatomic entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (polyatomic ion) + +AnnotationAssertion( "An ion consisting of more than one atom.") +AnnotationAssertion( "CHEBI:36358") +AnnotationAssertion(rdfs:label "polyatomic ion") +SubClassOf( ) +SubClassOf( ) + +# Class: (phosphorus oxoacid derivative) + +AnnotationAssertion( "CHEBI:36359") +AnnotationAssertion(rdfs:label "phosphorus oxoacid derivative") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus oxoacids and derivatives) + +AnnotationAssertion( "CHEBI:36360") +AnnotationAssertion(rdfs:label "phosphorus oxoacids and derivatives") +SubClassOf( ) + +# Class: (saturated organic heterocyclic parent) + +AnnotationAssertion( "CHEBI:36388") +AnnotationAssertion(rdfs:label "saturated organic heterocyclic parent") +SubClassOf( ) + +# Class: (saturated organic heteromonocyclic parent) + +AnnotationAssertion( "CHEBI:36389") +AnnotationAssertion(rdfs:label "saturated organic heteromonocyclic parent") +SubClassOf( ) +SubClassOf( ) + +# Class: (carbonyl compound) + +AnnotationAssertion( "Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.") +AnnotationAssertion( "CHEBI:36586") +AnnotationAssertion(rdfs:label "carbonyl compound") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic oxo compound) + +AnnotationAssertion( "Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.") +AnnotationAssertion( "CHEBI:36587") +AnnotationAssertion(rdfs:label "organic oxo compound") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (acid anhydride) + +AnnotationAssertion( "Compounds consisting of two acyl groups bonded to the same oxygen atom acyl-O-acyl.") +AnnotationAssertion( "CHEBI:36606") +AnnotationAssertion(rdfs:label "acid anhydride") +SubClassOf( ) + +# Class: (acyclic acid anhydride) + +AnnotationAssertion( "CHEBI:36608") +AnnotationAssertion(rdfs:label "acyclic acid anhydride") +SubClassOf( ) + +# Class: (organochlorine compound) + +AnnotationAssertion( "An organochlorine compound is a compound containing at least one carbon-chlorine bond.") +AnnotationAssertion( "CHEBI:36683") +AnnotationAssertion(rdfs:label "organochlorine compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (pseudohalo group) + +AnnotationAssertion( "CHEBI:36823") +AnnotationAssertion(rdfs:label "pseudohalo group") +SubClassOf( ) + +# Class: (pseudohalide anion) + +AnnotationAssertion( "CHEBI:36828") +AnnotationAssertion(rdfs:label "pseudohalide anion") +SubClassOf( ) + +# Class: (polyatomic monoanion) + +AnnotationAssertion( "CHEBI:36829") +AnnotationAssertion(rdfs:label "polyatomic monoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (monoanion) + +AnnotationAssertion( "CHEBI:36830") +AnnotationAssertion(rdfs:label "monoanion") +SubClassOf( ) + +# Class: (hydrogen isocyanide) + +AnnotationAssertion( "CHEBI:36856") +AnnotationAssertion(rdfs:label "hydrogen isocyanide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chalcogen hydride) + +AnnotationAssertion( "CHEBI:36902") +AnnotationAssertion(rdfs:label "chalcogen hydride") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic ion) + +AnnotationAssertion( "CHEBI:36914") +AnnotationAssertion(rdfs:label "inorganic ion") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic cation) + +AnnotationAssertion( "CHEBI:36915") +AnnotationAssertion(rdfs:label "inorganic cation") +SubClassOf( ) +SubClassOf( ) + +# Class: (cation) + +AnnotationAssertion( "A monoatomic or polyatomic species having one or more elementary charges of the proton.") +AnnotationAssertion( "CHEBI:36916") +AnnotationAssertion(rdfs:label "cation") +SubClassOf( ) + +# Class: (carbon-13 atom) + +AnnotationAssertion( "CHEBI:36928") +AnnotationAssertion(rdfs:label "carbon-13 atom") +SubClassOf( ) + +# Class: (chalcocarbonic acid) + +AnnotationAssertion( "CHEBI:36961") +AnnotationAssertion(rdfs:label "chalcocarbonic acid") +SubClassOf( ) + +# Class: (organochalcogen compound) + +AnnotationAssertion( "An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.") +AnnotationAssertion( "CHEBI:36962") +AnnotationAssertion(rdfs:label "organochalcogen compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (organooxygen compound) + +AnnotationAssertion( "An organochalcogen compound containing at least one carbon-oxygen bond.") +AnnotationAssertion( "CHEBI:36963") +AnnotationAssertion(rdfs:label "organooxygen compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (nucleotide) + +AnnotationAssertion( "A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid.") +AnnotationAssertion( "CHEBI:36976") +AnnotationAssertion(rdfs:label "nucleotide") +SubClassOf( ) + +# Class: (2'-deoxyribonucleoside 5'-phosphate) + +AnnotationAssertion( "CHEBI:37016") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleoside 5'-phosphate") +SubClassOf( ) +SubClassOf( ) + +# Class: (amino-acid anion) + +AnnotationAssertion( "CHEBI:37022") +AnnotationAssertion(rdfs:label "amino-acid anion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic hydride) + +AnnotationAssertion( "CHEBI:37175") +AnnotationAssertion(rdfs:label "organic hydride") +SubClassOf( ) + +# Class: (mononuclear parent hydride) + +AnnotationAssertion( "CHEBI:37176") +AnnotationAssertion(rdfs:label "mononuclear parent hydride") +SubClassOf( ) + +# Class: (elemental sodium) + +AnnotationAssertion( "CHEBI:37246") +AnnotationAssertion(rdfs:label "elemental sodium") +SubClassOf( ) + +# Class: (acid) + +AnnotationAssertion( "An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).") +AnnotationAssertion( "CHEBI:37527") +AnnotationAssertion(rdfs:label "acid") +SubClassOf( ) + +# Class: (heteroatomic molecular entity) + +AnnotationAssertion( "A molecular entity consisting of two or more chemical elements.") +AnnotationAssertion( "CHEBI:37577") +AnnotationAssertion(rdfs:label "heteroatomic molecular entity") +SubClassOf( ) + +# Class: (halide) + +AnnotationAssertion( "Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements.") +AnnotationAssertion( "CHEBI:37578") +AnnotationAssertion(rdfs:label "halide") +SubClassOf( ) +SubClassOf( ) + +# Class: (carboxamide) + +AnnotationAssertion( "An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.") +AnnotationAssertion( "CHEBI:37622") +AnnotationAssertion(rdfs:label "carboxamide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphoric ester) + +AnnotationAssertion( "CHEBI:37734") +AnnotationAssertion(rdfs:label "phosphoric ester") +SubClassOf( ) +SubClassOf( ) + +# Class: (acyclic phosphorus acid anhydride) + +AnnotationAssertion( "CHEBI:37786") +AnnotationAssertion(rdfs:label "acyclic phosphorus acid anhydride") +SubClassOf( ) + +# Class: (carboacyl group) + +AnnotationAssertion( "A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.") +AnnotationAssertion( "CHEBI:37838") +AnnotationAssertion(rdfs:label "carboacyl group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organonitrogen heterocyclic compound) + +AnnotationAssertion( "Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.") +AnnotationAssertion( "CHEBI:38101") +AnnotationAssertion(rdfs:label "organonitrogen heterocyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (oxacycle) + +AnnotationAssertion( "Any organic heterocyclic compound containing at least one ring oxygen atom.") +AnnotationAssertion( "CHEBI:38104") +AnnotationAssertion(rdfs:label "oxacycle") +SubClassOf( ) +SubClassOf( ) + +# Class: (organosulfur heterocyclic compound) + +AnnotationAssertion( "CHEBI:38106") +AnnotationAssertion(rdfs:label "organosulfur heterocyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic heteropolycyclic compound) + +AnnotationAssertion( "CHEBI:38166") +AnnotationAssertion(rdfs:label "organic heteropolycyclic compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (monocyclic heteroarene) + +AnnotationAssertion( "CHEBI:38179") +AnnotationAssertion(rdfs:label "monocyclic heteroarene") +SubClassOf( ) + +# Class: (hydrocarbyl anion) + +AnnotationAssertion( "CHEBI:38222") +AnnotationAssertion(rdfs:label "hydrocarbyl anion") +SubClassOf( ) + +# Class: (imidazolidines) + +AnnotationAssertion( "CHEBI:38261") +AnnotationAssertion(rdfs:label "imidazolidines") +SubClassOf( ) + +# Class: (azabicycloalkane) + +AnnotationAssertion( "CHEBI:38295") +AnnotationAssertion(rdfs:label "azabicycloalkane") +SubClassOf( ) +SubClassOf( ) + +# Class: (thiabicycloalkane) + +AnnotationAssertion( "CHEBI:38297") +AnnotationAssertion(rdfs:label "thiabicycloalkane") +SubClassOf( ) +SubClassOf( ) + +# Class: (diazolidine) + +AnnotationAssertion( "CHEBI:38304") +AnnotationAssertion(rdfs:label "diazolidine") +SubClassOf( ) +SubClassOf( ) + +# Class: (acetonitrile) + +AnnotationAssertion( "A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group.") +AnnotationAssertion( "CHEBI:38472") +AnnotationAssertion(rdfs:label "acetonitrile") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (electron-transport chain inhibitor) + +AnnotationAssertion( "CHEBI:38496") +AnnotationAssertion(rdfs:label "electron-transport chain inhibitor") +SubClassOf( ) + +# Class: (respiratory-chain inhibitor) + +AnnotationAssertion( "CHEBI:38497") +AnnotationAssertion(rdfs:label "respiratory-chain inhibitor") +SubClassOf( ) + +# Class: (EC 1.9.3.1 (cytochrome c oxidase) inhibitor) + +AnnotationAssertion( "An EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor that interferes with the action of cytochrome c oxidase (EC 1.9.3.1).") +AnnotationAssertion( "CHEBI:38500") +AnnotationAssertion(rdfs:label "EC 1.9.3.1 (cytochrome c oxidase) inhibitor") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic sodium salt) + +AnnotationAssertion( "CHEBI:38700") +AnnotationAssertion(rdfs:label "organic sodium salt") +SubClassOf( ) +SubClassOf( ) + +# Class: (inorganic sodium salt) + +AnnotationAssertion( "CHEBI:38702") +AnnotationAssertion(rdfs:label "inorganic sodium salt") +SubClassOf( ) +SubClassOf( ) + +# Class: (morpholines) + +AnnotationAssertion( "Any compound containing morpholine as part of its structure.") +AnnotationAssertion( "CHEBI:38785") +AnnotationAssertion(rdfs:label "morpholines") +SubClassOf( ) + +# Class: (anaesthetic) + +AnnotationAssertion( "Substance which produces loss of feeling or sensation.") +AnnotationAssertion( "CHEBI:38867") +AnnotationAssertion(rdfs:label "anaesthetic") +SubClassOf( ) + +# Class: (general anaesthetic) + +AnnotationAssertion( "Substance that produces loss of consciousness.") +AnnotationAssertion( "CHEBI:38869") +AnnotationAssertion(rdfs:label "general anaesthetic") +SubClassOf( ) + +# Class: (inhalation anaesthetic) + +AnnotationAssertion( "CHEBI:38870") +AnnotationAssertion(rdfs:label "inhalation anaesthetic") +SubClassOf( ) + +# Class: (Bronsted acid) + +AnnotationAssertion( "A molecular entity capable of donating a hydron to an acceptor (Bronsted base).") +AnnotationAssertion( "CHEBI:39141") +AnnotationAssertion(rdfs:label "Bronsted acid") +SubClassOf( ) +SubClassOf( ) + +# Class: (Bronsted base) + +AnnotationAssertion( "A molecular entity capable of accepting a hydron from a donor (Bronsted acid).") +AnnotationAssertion( "CHEBI:39142") +AnnotationAssertion(rdfs:label "Bronsted base") +SubClassOf( ) +SubClassOf( ) + +# Class: (Lewis base) + +AnnotationAssertion( "A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.") +AnnotationAssertion( "CHEBI:39144") +AnnotationAssertion(rdfs:label "Lewis base") +SubClassOf( ) +SubClassOf( ) + +# Class: (halomethane) + +AnnotationAssertion( "A haloalkane that is methane in which one (or more) of the hydrogens have been replaced by a halogen atom/halogen atoms.") +AnnotationAssertion( "CHEBI:39279") +AnnotationAssertion(rdfs:label "halomethane") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (dihydrogenphosphate) + +AnnotationAssertion( "A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.") +AnnotationAssertion( "CHEBI:39745") +AnnotationAssertion(rdfs:label "dihydrogenphosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbonate) + +AnnotationAssertion( "CHEBI:41609") +AnnotationAssertion(rdfs:label "carbonate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (dideuterium oxide) + +AnnotationAssertion( "CHEBI:41981") +AnnotationAssertion(rdfs:label "dideuterium oxide") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydroxy group) + +AnnotationAssertion( "CHEBI:43176") +AnnotationAssertion(rdfs:label "hydroxy group") +SubClassOf( ) + +# Class: (hydrogenphosphate) + +AnnotationAssertion( "A phosphate ion that is the conjugate base of dihydrogenphosphate.") +AnnotationAssertion( "CHEBI:43474") +AnnotationAssertion(rdfs:label "hydrogenphosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (deoxyribonucleotide) + +AnnotationAssertion( "A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen.") +AnnotationAssertion( "CHEBI:4431") +AnnotationAssertion(rdfs:label "deoxyribonucleotide") +SubClassOf( ) +SubClassOf( ) + +# Class: (diphosphate(2-)) + +AnnotationAssertion( "A divalent inorganic anion obtained by removal of both protons from diphosphoric acid.") +AnnotationAssertion( "CHEBI:45212") +AnnotationAssertion(rdfs:label "diphosphate(2-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxo group) + +AnnotationAssertion( "CHEBI:46629") +AnnotationAssertion(rdfs:label "oxo group") +SubClassOf( ) + +# Class: (solvent) + +AnnotationAssertion( "A liquid that can dissolve other substances (solutes) without any change in their chemical composition.") +AnnotationAssertion( "CHEBI:46787") +AnnotationAssertion(rdfs:label "solvent") +SubClassOf( ) +SubClassOf( ) + +# Class: (carboxy group) + +AnnotationAssertion( "CHEBI:46883") +AnnotationAssertion(rdfs:label "carboxy group") +SubClassOf( ) + +# Class: (dioxane) + +AnnotationAssertion( "Any member of the class of dioxanes that is a cyclohexane in which two carbon atoms are replaced by oxygen atoms.") +AnnotationAssertion( "CHEBI:46923") +AnnotationAssertion(rdfs:label "dioxane") +SubClassOf( ) +SubClassOf( ) + +# Class: (dioxanes) + +AnnotationAssertion( "CHEBI:46926") +AnnotationAssertion(rdfs:label "dioxanes") +SubClassOf( ) +SubClassOf( ) + +# Class: (oxazinane) + +AnnotationAssertion( "CHEBI:46952") +AnnotationAssertion(rdfs:label "oxazinane") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (tetrahydrofuranol) + +AnnotationAssertion( "CHEBI:47017") +AnnotationAssertion(rdfs:label "tetrahydrofuranol") +SubClassOf( ) + +# Class: (monohydroxytetrahydrofuran) + +AnnotationAssertion( "CHEBI:47018") +AnnotationAssertion(rdfs:label "monohydroxytetrahydrofuran") +SubClassOf( ) + +# Class: (1,4-dioxane) + +AnnotationAssertion( "A dioxane with oxygen atoms at positions 1 and 4.") +AnnotationAssertion( "CHEBI:47032") +AnnotationAssertion(rdfs:label "1,4-dioxane") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (double-stranded DNA) + +AnnotationAssertion( "CHEBI:4705") +AnnotationAssertion(rdfs:label "double-stranded DNA") +SubClassOf( ) + +# Class: (ureas) + +AnnotationAssertion( "CHEBI:47857") +AnnotationAssertion(rdfs:label "ureas") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitric acid) + +AnnotationAssertion( "A nitrogen oxoacid of formula HNO3 in which the nitrogen atom is bonded to a hydroxy group and by equivalent bonds to the remaining two oxygen atoms.") +AnnotationAssertion( "CHEBI:48107") +AnnotationAssertion(rdfs:label "nitric acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sulfur oxide) + +AnnotationAssertion( "CHEBI:48154") +AnnotationAssertion(rdfs:label "sulfur oxide") +SubClassOf( ) +SubClassOf( ) + +# Class: (polar solvent) + +AnnotationAssertion( "A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.") +AnnotationAssertion( "CHEBI:48354") +AnnotationAssertion(rdfs:label "polar solvent") +SubClassOf( ) + +# Class: (non-polar solvent) + +AnnotationAssertion( "CHEBI:48355") +AnnotationAssertion(rdfs:label "non-polar solvent") +SubClassOf( ) + +# Class: (protic solvent) + +AnnotationAssertion( "A polar solvent that is capable of acting as a hydron (proton) donor.") +AnnotationAssertion( "CHEBI:48356") +AnnotationAssertion(rdfs:label "protic solvent") +SubClassOf( ) +SubClassOf( ) + +# Class: (aprotic solvent) + +AnnotationAssertion( "CHEBI:48357") +AnnotationAssertion(rdfs:label "aprotic solvent") +SubClassOf( ) + +# Class: (polar aprotic solvent) + +AnnotationAssertion( "A solvent with a comparatively high relative permittivity (or dielectric constant), greater than ca. 15, and a sizable permanent dipole moment, that cannot donate suitably labile hydrogen atoms to form strong hydrogen bonds.") +AnnotationAssertion( "CHEBI:48358") +AnnotationAssertion(rdfs:label "polar aprotic solvent") +SubClassOf( ) +SubClassOf( ) + +# Class: (protophilic solvent) + +AnnotationAssertion( "Solvent that is capable of acting as a hydron (proton) acceptor.") +AnnotationAssertion( "CHEBI:48359") +AnnotationAssertion(rdfs:label "protophilic solvent") +SubClassOf( ) +SubClassOf( ) + +# Class: (amphiprotic solvent) + +AnnotationAssertion( "Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.") +AnnotationAssertion( "CHEBI:48360") +AnnotationAssertion(rdfs:label "amphiprotic solvent") +SubClassOf( ) +SubClassOf( ) + +# Class: (carbamimidic acid) + +AnnotationAssertion( "CHEBI:48376") +AnnotationAssertion(rdfs:label "carbamimidic acid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (imidic acid) + +AnnotationAssertion( "Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH).") +AnnotationAssertion( "CHEBI:48377") +AnnotationAssertion(rdfs:label "imidic acid") +SubClassOf( ) +SubClassOf( ) + +# Class: (carboximidic acid) + +AnnotationAssertion( "CHEBI:48378") +AnnotationAssertion(rdfs:label "carboximidic acid") +SubClassOf( ) +SubClassOf( ) + +# Class: (isourea) + +AnnotationAssertion( "A carboximidic acid that is the imidic acid tautomer of urea, H2NC(=NH)OH, and its hydrocarbyl derivatives.") +AnnotationAssertion( "CHEBI:48379") +AnnotationAssertion(rdfs:label "isourea") +SubClassOf( ) + +# Class: (cyano group) + +AnnotationAssertion( "CHEBI:48819") +AnnotationAssertion(rdfs:label "cyano group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sulfurous acid) + +AnnotationAssertion( "CHEBI:48854") +AnnotationAssertion(rdfs:label "sulfurous acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrogen atom) + +AnnotationAssertion( "CHEBI:49637") +AnnotationAssertion(rdfs:label "hydrogen atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic amino compound) + +AnnotationAssertion( "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.") +AnnotationAssertion( "CHEBI:50047") +AnnotationAssertion(rdfs:label "organic amino compound") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (excitatory amino acid agonist) + +AnnotationAssertion( "An agent that binds to and activates excitatory amino acid receptors.") +AnnotationAssertion( "CHEBI:50103") +AnnotationAssertion(rdfs:label "excitatory amino acid agonist") +SubClassOf( ) + +# Class: (protective agent) + +AnnotationAssertion( "Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent.") +AnnotationAssertion( "CHEBI:50267") +AnnotationAssertion(rdfs:label "protective agent") +SubClassOf( ) + +# Class: (canonical nucleotide residue) + +AnnotationAssertion( "CHEBI:50297") +AnnotationAssertion(rdfs:label "canonical nucleotide residue") +SubClassOf( ) + +# Class: (canonical deoxyribonucleotide residue) + +AnnotationAssertion( "CHEBI:50298") +AnnotationAssertion(rdfs:label "canonical deoxyribonucleotide residue") +SubClassOf( ) + +# Class: (canonical ribonucleotide residue) + +AnnotationAssertion( "CHEBI:50299") +AnnotationAssertion(rdfs:label "canonical ribonucleotide residue") +SubClassOf( ) + +# Class: (onium compound) + +AnnotationAssertion( "CHEBI:50312") +AnnotationAssertion(rdfs:label "onium compound") +SubClassOf( ) + +# Class: (onium cation) + +AnnotationAssertion( "Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.") +AnnotationAssertion( "CHEBI:50313") +AnnotationAssertion(rdfs:label "onium cation") +SubClassOf( ) + +# Class: (nucleotide residue) + +AnnotationAssertion( "CHEBI:50319") +AnnotationAssertion(rdfs:label "nucleotide residue") +SubClassOf( ) + +# Class: (nucleoside residue) + +AnnotationAssertion( "CHEBI:50320") +AnnotationAssertion(rdfs:label "nucleoside residue") +SubClassOf( ) + +# Class: (nutraceutical) + +AnnotationAssertion( "A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance.") +AnnotationAssertion( "CHEBI:50733") +AnnotationAssertion(rdfs:label "nutraceutical") +SubClassOf( ) + +# Class: (organic molecular entity) + +AnnotationAssertion( "Any molecular entity that contains carbon.") +AnnotationAssertion( "CHEBI:50860") +AnnotationAssertion(rdfs:label "organic molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (azaarene) + +AnnotationAssertion( "CHEBI:50893") +AnnotationAssertion(rdfs:label "azaarene") +SubClassOf( ) +SubClassOf( ) + +# Class: (carcinogenic agent) + +AnnotationAssertion( "A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities.") +AnnotationAssertion( "CHEBI:50903") +AnnotationAssertion(rdfs:label "carcinogenic agent") +SubClassOf( ) + +# Class: (role) + +AnnotationAssertion( "A role is particular behaviour which a material entity may exhibit.") +AnnotationAssertion( "CHEBI:50906") +AnnotationAssertion(rdfs:label "role") + +# Class: (neurotoxin) + +AnnotationAssertion( "A poison that interferes with the functions of the nervous system.") +AnnotationAssertion( "CHEBI:50910") +AnnotationAssertion(rdfs:label "neurotoxin") +SubClassOf( ) +SubClassOf( ) + +# Class: (secondary amino compound) + +AnnotationAssertion( "A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups.") +AnnotationAssertion( "CHEBI:50995") +AnnotationAssertion(rdfs:label "secondary amino compound") +SubClassOf( ) + +# Class: (nitrate salt) + +AnnotationAssertion( "CHEBI:51082") +AnnotationAssertion(rdfs:label "nitrate salt") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (inorganic nitrate salt) + +AnnotationAssertion( "CHEBI:51084") +AnnotationAssertion(rdfs:label "inorganic nitrate salt") +SubClassOf( ) +SubClassOf( ) + +# Class: (chemical role) + +AnnotationAssertion( "A role played by the molecular entity or part thereof within a chemical context.") +AnnotationAssertion( "CHEBI:51086") +AnnotationAssertion(rdfs:label "chemical role") +SubClassOf( ) + +# Class: (nitrohydrocarbon) + +AnnotationAssertion( "A C-nitro compound that is a hydrocarbon in which one or more of the hydrogens has been replaced by nitro groups.") +AnnotationAssertion( "CHEBI:51129") +AnnotationAssertion(rdfs:label "nitrohydrocarbon") +SubClassOf( ) + +# Class: (nitrogen molecular entity) + +AnnotationAssertion( "CHEBI:51143") +AnnotationAssertion(rdfs:label "nitrogen molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrogen group) + +AnnotationAssertion( "CHEBI:51144") +AnnotationAssertion(rdfs:label "nitrogen group") +SubClassOf( ) + +# Class: (dipolar compound) + +AnnotationAssertion( "An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.") +AnnotationAssertion( "CHEBI:51151") +AnnotationAssertion(rdfs:label "dipolar compound") +SubClassOf( ) + +# Class: (organodiyl group) + +AnnotationAssertion( "Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).") +AnnotationAssertion( "CHEBI:51422") +AnnotationAssertion(rdfs:label "organodiyl group") +SubClassOf( ) + +# Class: (organic divalent group) + +AnnotationAssertion( "CHEBI:51446") +AnnotationAssertion(rdfs:label "organic divalent group") +SubClassOf( ) + +# Class: (organic univalent group) + +AnnotationAssertion( "CHEBI:51447") +AnnotationAssertion(rdfs:label "organic univalent group") +SubClassOf( ) + +# Class: (biotins) + +AnnotationAssertion( "Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton.") +AnnotationAssertion( "CHEBI:51570") +AnnotationAssertion(rdfs:label "biotins") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (biochemical role) + +AnnotationAssertion( "A biological role played by the molecular entity or part thereof within a biochemical context.") +AnnotationAssertion( "CHEBI:52206") +AnnotationAssertion(rdfs:label "biochemical role") +SubClassOf( ) + +# Class: (aetiopathogenetic role) + +AnnotationAssertion( "A role played by the molecular entity or part thereof which causes the development of a pathological process.") +AnnotationAssertion( "CHEBI:52209") +AnnotationAssertion(rdfs:label "aetiopathogenetic role") +SubClassOf( ) + +# Class: (pharmacological role) + +AnnotationAssertion( "A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.") +AnnotationAssertion( "CHEBI:52210") +AnnotationAssertion(rdfs:label "pharmacological role") +SubClassOf( ) + +# Class: (physiological role) + +AnnotationAssertion( "CHEBI:52211") +AnnotationAssertion(rdfs:label "physiological role") +SubClassOf( ) + +# Class: (pharmaceutical) + +AnnotationAssertion( "Any substance introduced into a living organism with therapeutic or diagnostic purpose.") +AnnotationAssertion( "CHEBI:52217") +AnnotationAssertion(rdfs:label "pharmaceutical") +SubClassOf( ) + +# Class: (inorganic hydroxy compound) + +AnnotationAssertion( "CHEBI:52625") +AnnotationAssertion(rdfs:label "inorganic hydroxy compound") +SubClassOf( ) +SubClassOf( ) + +# Class: (sodium-23 atom) + +AnnotationAssertion( "The stable isotope of sodium with relative atomic mass 22.989770, 100 atom percent natural abundance and nuclear spin 3/2.") +AnnotationAssertion( "CHEBI:52634") +AnnotationAssertion(rdfs:label "sodium-23 atom") +SubClassOf( ) + +# Class: (ionic macromolecule) + +AnnotationAssertion( "A macromolecule containing ionic groups.") +AnnotationAssertion( "CHEBI:53368") +AnnotationAssertion(rdfs:label "ionic macromolecule") +SubClassOf( ) + +# Class: (imidazolidinone) + +AnnotationAssertion( "An imidazolidine containing one or more oxo groups.") +AnnotationAssertion( "CHEBI:55370") +AnnotationAssertion(rdfs:label "imidazolidinone") +SubClassOf( ) + +# Class: (heterocyclic compound) + +AnnotationAssertion( "A cyclic compound having as ring members atoms of at least two different elements.") +AnnotationAssertion( "CHEBI:5686") +AnnotationAssertion(rdfs:label "heterocyclic compound") +SubClassOf( ) + +# Class: (hexachlorobenzene) + +AnnotationAssertion( "A member of the class of chlorobenzenes that is benzene in which all of the hydrogens are replaced by chlorines. An agricultural fungicide introduced in the mid-1940s and formerly used as a seed treatment, its use has been banned since 1984 under the Stockholm Convention on Persistent Organic Pollutants.") +AnnotationAssertion( "CHEBI:5692") +AnnotationAssertion(rdfs:label "hexachlorobenzene") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycine zwitterion) + +AnnotationAssertion( "An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine.") +AnnotationAssertion( "CHEBI:57305") +AnnotationAssertion(rdfs:label "glycine zwitterion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biotinate) + +AnnotationAssertion( "Conjugate base of biotin arising from deprotonation of the carboxy group.") +AnnotationAssertion( "CHEBI:57586") +AnnotationAssertion(rdfs:label "biotinate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside 5'-phosphate dianion) + +AnnotationAssertion( "The conjugate base of a nucleoside 5'-phosphate.") +AnnotationAssertion( "CHEBI:57867") +AnnotationAssertion(rdfs:label "nucleoside 5'-phosphate dianion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatine zwitterion) + +AnnotationAssertion( "Zwitterionic form of creatine arising from transfer of a proton from the carboxy to the guanidino group; major species at pH 7.3.") +AnnotationAssertion( "CHEBI:57947") +AnnotationAssertion(rdfs:label "creatine zwitterion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cationic amino-acid residue) + +AnnotationAssertion( "An amino-acid residue protonated on nitrogen.") +AnnotationAssertion( "CHEBI:58942") +AnnotationAssertion(rdfs:label "cationic amino-acid residue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organophosphate oxoanion) + +AnnotationAssertion( "An organic phosphoric acid derivative in which one or more oxygen atoms of the phosphate group(s) has been deprotonated.") +AnnotationAssertion( "CHEBI:58945") +AnnotationAssertion(rdfs:label "organophosphate oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (phosphoric acids) + +AnnotationAssertion( "Compounds containing one or more phosphoric acid units.") +AnnotationAssertion( "CHEBI:59698") +AnnotationAssertion(rdfs:label "phosphoric acids") +SubClassOf( ) + +# Class: (nucleophilic reagent) + +AnnotationAssertion( "A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.") +AnnotationAssertion( "CHEBI:59740") +AnnotationAssertion(rdfs:label "nucleophilic reagent") +SubClassOf( ) +SubClassOf( ) + +# Class: (chemical substance) + +AnnotationAssertion( "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.") +AnnotationAssertion( "CHEBI:59999") +AnnotationAssertion(rdfs:label "chemical substance") +SubClassOf( ) + +# Class: (mixture) + +AnnotationAssertion( "A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.") +AnnotationAssertion( "CHEBI:60004") +AnnotationAssertion(rdfs:label "mixture") +SubClassOf( ) + +# Class: (polymer) + +AnnotationAssertion( "A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..") +AnnotationAssertion( "CHEBI:60027") +AnnotationAssertion(rdfs:label "polymer") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ionic polymer) + +AnnotationAssertion( "An ionic polymer is a polymer, composed of ionic macromolecules.") +AnnotationAssertion( "CHEBI:60164") +AnnotationAssertion(rdfs:label "ionic polymer") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monovalent inorganic cation) + +AnnotationAssertion( "An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.") +AnnotationAssertion( "CHEBI:60242") +AnnotationAssertion(rdfs:label "monovalent inorganic cation") +SubClassOf( ) + +# Class: (peptide zwitterion) + +AnnotationAssertion( "Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.") +AnnotationAssertion( "CHEBI:60466") +AnnotationAssertion(rdfs:label "peptide zwitterion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase-containing molecular entity) + +AnnotationAssertion( "Any compound that has a nucleobase as a part.") +AnnotationAssertion( "CHEBI:61120") +AnnotationAssertion(rdfs:label "nucleobase-containing molecular entity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleoside 5'-triphosphate(4-)) + +AnnotationAssertion( "A 2'-deoxyribonucleoside triphosphate oxoanion being the tetraanion formed by global deprotonation of the triphosphate group.") +AnnotationAssertion( "CHEBI:61560") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleoside 5'-triphosphate(4-)") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleoside triphosphate oxoanion) + +AnnotationAssertion( "An organophosphate anion resulting from deprotonation of at least one of the acidic hydroxy groups from the triphosphate moiety of a 2'-deoxyribonucleoside triphosphate.") +AnnotationAssertion( "CHEBI:61662") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleoside triphosphate oxoanion") +SubClassOf( ) + +# Class: (reactive nitrogen species) + +AnnotationAssertion( "A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively.") +AnnotationAssertion( "CHEBI:62764") +AnnotationAssertion(rdfs:label "reactive nitrogen species") +SubClassOf( ) + +# Class: (hepatoprotective agent) + +AnnotationAssertion( "Any compound that is able to prevent damage to the liver.") +AnnotationAssertion( "CHEBI:62868") +AnnotationAssertion(rdfs:label "hepatoprotective agent") +SubClassOf( ) + +# Class: (sodium nitrate) + +AnnotationAssertion( "The inorganic nitrate salt of sodium.") +AnnotationAssertion( "CHEBI:63005") +AnnotationAssertion(rdfs:label "sodium nitrate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycosyl compound) + +AnnotationAssertion( "A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity.") +AnnotationAssertion( "CHEBI:63161") +AnnotationAssertion(rdfs:label "glycosyl compound") +SubClassOf( ) + +# Class: (carbohydrate derivative) + +AnnotationAssertion( "Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.") +AnnotationAssertion( "CHEBI:63299") +AnnotationAssertion(rdfs:label "carbohydrate derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monosaccharide derivative) + +AnnotationAssertion( "A carbohydrate derivative that is formally obtained from a monosaccharide.") +AnnotationAssertion( "CHEBI:63367") +AnnotationAssertion(rdfs:label "monosaccharide derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pentose derivative) + +AnnotationAssertion( "A monosaccharide derivative that is formally obtained from a pentose.") +AnnotationAssertion( "CHEBI:63409") +AnnotationAssertion(rdfs:label "pentose derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (explosive) + +AnnotationAssertion( "A substance capable of undergoing rapid and highly exothermic decomposition.") +AnnotationAssertion( "CHEBI:63490") +AnnotationAssertion(rdfs:label "explosive") +SubClassOf( ) + +# Class: (neuroprotective agent) + +AnnotationAssertion( "Any compound that can be used for the treatment of neurodegenerative disorders.") +AnnotationAssertion( "CHEBI:63726") +AnnotationAssertion(rdfs:label "neuroprotective agent") +SubClassOf( ) + +# Class: (food additive) + +AnnotationAssertion( "Any substance which is added to food to preserve or enhance its flavour and/or appearance.") +AnnotationAssertion( "CHEBI:64047") +AnnotationAssertion(rdfs:label "food additive") +SubClassOf( ) +SubClassOf( ) + +# Class: (food acidity regulator) + +AnnotationAssertion( "A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents.") +AnnotationAssertion( "CHEBI:64049") +AnnotationAssertion(rdfs:label "food acidity regulator") +SubClassOf( ) + +# Class: (EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor) + +AnnotationAssertion( "An EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor that interferes with the action of glycine hydroxymethyltransferase (EC 2.1.2.1).") +AnnotationAssertion( "CHEBI:64570") +AnnotationAssertion(rdfs:label "EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor") +SubClassOf( ) + +# Class: (NMDA receptor agonist) + +AnnotationAssertion( "An excitatory amino acid agonist which binds to NMDA receptors and triggers a response.") +AnnotationAssertion( "CHEBI:64571") +AnnotationAssertion(rdfs:label "NMDA receptor agonist") +SubClassOf( ) + +# Class: (flour treatment agent) + +AnnotationAssertion( "A food additive which is added to flour or dough to improve baking quality and/or colour.") +AnnotationAssertion( "CHEBI:64577") +AnnotationAssertion(rdfs:label "flour treatment agent") +SubClassOf( ) + +# Class: (one-carbon compound) + +AnnotationAssertion( "An organic molecular entity containing a single carbon atom (C1).") +AnnotationAssertion( "CHEBI:64708") +AnnotationAssertion(rdfs:label "one-carbon compound") +SubClassOf( ) + +# Class: (organic acid) + +AnnotationAssertion( "Any organic molecular entity that is acidic and contains carbon in covalent linkage.") +AnnotationAssertion( "CHEBI:64709") +AnnotationAssertion(rdfs:label "organic acid") +SubClassOf( ) + +# Class: (cationic group) + +AnnotationAssertion( "A group that carries an overall positive charge.") +AnnotationAssertion( "CHEBI:64766") +AnnotationAssertion(rdfs:label "cationic group") +SubClassOf( ) + +# Class: (anionic group) + +AnnotationAssertion( "A group that carries an overall negative charge.") +AnnotationAssertion( "CHEBI:64767") +AnnotationAssertion(rdfs:label "anionic group") +SubClassOf( ) + +# Class: (organic cationic group) + +AnnotationAssertion( "A cationic group that contains carbon.") +AnnotationAssertion( "CHEBI:64769") +AnnotationAssertion(rdfs:label "organic cationic group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic anionic group) + +AnnotationAssertion( "An anionic group that contains carbon.") +AnnotationAssertion( "CHEBI:64775") +AnnotationAssertion(rdfs:label "organic anionic group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anionic amino-acid residue) + +AnnotationAssertion( "An amino-acid residue carrying an overall negative charge.") +AnnotationAssertion( "CHEBI:64898") +AnnotationAssertion(rdfs:label "anionic amino-acid residue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (poison) + +AnnotationAssertion( "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.") +AnnotationAssertion( "CHEBI:64909") +AnnotationAssertion(rdfs:label "poison") +SubClassOf( ) + +# Class: (food preservative) + +AnnotationAssertion( "Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.") +AnnotationAssertion( "CHEBI:65255") +AnnotationAssertion(rdfs:label "food preservative") +SubClassOf( ) + +# Class: (antimicrobial food preservative) + +AnnotationAssertion( "A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299).") +AnnotationAssertion( "CHEBI:65256") +AnnotationAssertion(rdfs:label "antimicrobial food preservative") +SubClassOf( ) +SubClassOf( ) + +# Class: (creatinate) + +AnnotationAssertion( "A monocarboxylic acid anion that is the conjugate base of creatine, obtained by deprotonation of the carboxy group.") +AnnotationAssertion( "CHEBI:66924") +AnnotationAssertion(rdfs:label "creatinate") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (EC 2.* (transferase) inhibitor) + +AnnotationAssertion( "An enzyme inhibitor that inhibits the action of a transferase (EC 2.*)") +AnnotationAssertion( "CHEBI:71300") +AnnotationAssertion(rdfs:label "EC 2.* (transferase) inhibitor") +SubClassOf( ) + +# Class: (flavonoids) + +AnnotationAssertion( "Any organic molecular entity whose stucture is based on derivatives of a phenyl-substituted 1-phenylpropane possessing a C15 or C16 skeleton, or such a structure which is condensed with a C6-C3 lignan precursors. The term is a 'superclass' comprising all members of the classes of flavonoid, isoflavonoid, neoflavonoid, chalcones, dihydrochalcones, aurones, pterocarpan, coumestans, rotenoid, flavonolignan, homoflavonoid and flavonoid oligomers. Originally restricted to natural products, the term is also applied to synthetic compounds related to them.") +AnnotationAssertion( "CHEBI:72544") +AnnotationAssertion(rdfs:label "flavonoids") +SubClassOf( ) +SubClassOf( ) + +# Class: (organic molecule) + +AnnotationAssertion( "Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.") +AnnotationAssertion( "CHEBI:72695") +AnnotationAssertion(rdfs:label "organic molecule") +SubClassOf( ) +SubClassOf( ) + +# Class: (eukaryotic metabolite) + +AnnotationAssertion( "Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.") +AnnotationAssertion( "CHEBI:75763") +AnnotationAssertion(rdfs:label "eukaryotic metabolite") +SubClassOf( ) + +# Class: (animal metabolite) + +AnnotationAssertion( "Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.") +AnnotationAssertion( "CHEBI:75767") +AnnotationAssertion(rdfs:label "animal metabolite") +SubClassOf( ) + +# Class: (mammalian metabolite) + +AnnotationAssertion( "Any animal metabolite produced during a metabolic reaction in mammals.") +AnnotationAssertion( "CHEBI:75768") +AnnotationAssertion(rdfs:label "mammalian metabolite") +SubClassOf( ) + +# Class: (B vitamin) + +AnnotationAssertion( "Any member of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such).") +AnnotationAssertion( "CHEBI:75769") +AnnotationAssertion(rdfs:label "B vitamin") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mouse metabolite) + +AnnotationAssertion( "Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).") +AnnotationAssertion( "CHEBI:75771") +AnnotationAssertion(rdfs:label "mouse metabolite") +SubClassOf( ) + +# Class: (Saccharomyces cerevisiae metabolite) + +AnnotationAssertion( "Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).") +AnnotationAssertion( "CHEBI:75772") +AnnotationAssertion(rdfs:label "Saccharomyces cerevisiae metabolite") +SubClassOf( ) + +# Class: (prokaryotic metabolite) + +AnnotationAssertion( "Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.") +AnnotationAssertion( "CHEBI:75787") +AnnotationAssertion(rdfs:label "prokaryotic metabolite") +SubClassOf( ) + +# Class: (nitroalkane) + +AnnotationAssertion( "A nitrohydrocarbon that is an alkane in which one of the hydrogens has been replaced by a nitro group.") +AnnotationAssertion( "CHEBI:7587") +AnnotationAssertion(rdfs:label "nitroalkane") +SubClassOf( ) + +# Class: (deuterated compound) + +AnnotationAssertion( "Any isotopically modified compound that has one or more hydrogen atoms replaced by deuterium.") +AnnotationAssertion( "CHEBI:76107") +AnnotationAssertion(rdfs:label "deuterated compound") +SubClassOf( ) + +# Class: (greenhouse gas) + +AnnotationAssertion( "A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.") +AnnotationAssertion( "CHEBI:76413") +AnnotationAssertion(rdfs:label "greenhouse gas") +SubClassOf( ) + +# Class: (EC 2.1.* (C1-transferase) inhibitor) + +AnnotationAssertion( "A transferase inhibitor inhibiting the action of transferase of a one-carbon-containing group (EC 2.1.*.*).") +AnnotationAssertion( "CHEBI:76655") +AnnotationAssertion(rdfs:label "EC 2.1.* (C1-transferase) inhibitor") +SubClassOf( ) + +# Class: (EC 4.* (lyase) inhibitor) + +AnnotationAssertion( "An enzyme inhibitor which interferes with the action of a lyase (EC 4.*.*.*). Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation.") +AnnotationAssertion( "CHEBI:76710") +AnnotationAssertion(rdfs:label "EC 4.* (lyase) inhibitor") +SubClassOf( ) + +# Class: (EC 4.3.* (C-N lyase) inhibitor) + +AnnotationAssertion( "A lyase inhibitor which inhibits the action of a C-N lyase (EC 4.3.*.*).") +AnnotationAssertion( "CHEBI:76713") +AnnotationAssertion(rdfs:label "EC 4.3.* (C-N lyase) inhibitor") +SubClassOf( ) + +# Class: (EC 1.* (oxidoreductase) inhibitor) + +AnnotationAssertion( "An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).") +AnnotationAssertion( "CHEBI:76725") +AnnotationAssertion(rdfs:label "EC 1.* (oxidoreductase) inhibitor") +SubClassOf( ) + +# Class: (EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor) + +AnnotationAssertion( "An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).") +AnnotationAssertion( "CHEBI:76736") +AnnotationAssertion(rdfs:label "EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor") +SubClassOf( ) + +# Class: (EC 3.* (hydrolase) inhibitor) + +AnnotationAssertion( "Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).") +AnnotationAssertion( "CHEBI:76759") +AnnotationAssertion(rdfs:label "EC 3.* (hydrolase) inhibitor") +SubClassOf( ) + +# Class: (EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor) + +AnnotationAssertion( "Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).") +AnnotationAssertion( "CHEBI:76764") +AnnotationAssertion(rdfs:label "EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor") +SubClassOf( ) + +# Class: (EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor) + +AnnotationAssertion( "An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).") +AnnotationAssertion( "CHEBI:76807") +AnnotationAssertion(rdfs:label "EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor") +SubClassOf( ) + +# Class: (EC 4.3.1.* (ammonia-lyase) inhibitor) + +AnnotationAssertion( "An EC 4.3.* (C-N lyase) inhibitor that interferes with the action of any ammonia-lyase (EC 4.3.1.*).") +AnnotationAssertion( "CHEBI:76832") +AnnotationAssertion(rdfs:label "EC 4.3.1.* (ammonia-lyase) inhibitor") +SubClassOf( ) + +# Class: (EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor) + +AnnotationAssertion( "An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).") +AnnotationAssertion( "CHEBI:76870") +AnnotationAssertion(rdfs:label "EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor") +SubClassOf( ) + +# Class: (EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor) + +AnnotationAssertion( "An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any hydroxymethyl-, formyl- and related transferase (EC 2.1.2.*).") +AnnotationAssertion( "CHEBI:76874") +AnnotationAssertion(rdfs:label "EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor") +SubClassOf( ) + +# Class: (pathway inhibitor) + +AnnotationAssertion( "An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.") +AnnotationAssertion( "CHEBI:76932") +AnnotationAssertion(rdfs:label "pathway inhibitor") +SubClassOf( ) + +# Class: (fungal metabolite) + +AnnotationAssertion( "Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.") +AnnotationAssertion( "CHEBI:76946") +AnnotationAssertion(rdfs:label "fungal metabolite") +SubClassOf( ) + +# Class: (bacterial metabolite) + +AnnotationAssertion( "Any prokaryotic metabolite produced during a metabolic reaction in bacteria.") +AnnotationAssertion( "CHEBI:76969") +AnnotationAssertion(rdfs:label "bacterial metabolite") +SubClassOf( ) + +# Class: (Escherichia coli metabolite) + +AnnotationAssertion( "Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.") +AnnotationAssertion( "CHEBI:76971") +AnnotationAssertion(rdfs:label "Escherichia coli metabolite") +SubClassOf( ) + +# Class: (nitromethane) + +AnnotationAssertion( "A primary nitroalkane that is methane in which one of the hydrogens is replace by a nitro group. A polar solvent (b.p. 101 degreeC), it is an important starting material in organic synthesis. It is also used as a fuel for rockets and radio-controlled models.") +AnnotationAssertion( "CHEBI:77701") +AnnotationAssertion(rdfs:label "nitromethane") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (EC 4.3.1.3 (histidine ammonia-lyase) inhibitor) + +AnnotationAssertion( "An EC 4.3.1.* (ammonia-lyase) inhibitor that interferes with the action of histidine ammonia-lyase (EC 4.3.1.3).") +AnnotationAssertion( "CHEBI:77703") +AnnotationAssertion(rdfs:label "EC 4.3.1.3 (histidine ammonia-lyase) inhibitor") +SubClassOf( ) + +# Class: (human metabolite) + +AnnotationAssertion( "Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).") +AnnotationAssertion( "CHEBI:77746") +AnnotationAssertion(rdfs:label "human metabolite") +SubClassOf( ) + +# Class: (persistent organic pollutant) + +AnnotationAssertion( "Any environmental contaminant that is resistant to environmental degradation through photolytic, biological or chemical processes. Such substances can have significant impact on health and the environment, as they persist in the environment, bioaccumulate in animal tissue and so biomagnify in food chains.") +AnnotationAssertion( "CHEBI:77853") +AnnotationAssertion(rdfs:label "persistent organic pollutant") +SubClassOf( ) + +# Class: (EC 3.5.1.4 (amidase) inhibitor) + +AnnotationAssertion( "An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).") +AnnotationAssertion( "CHEBI:77941") +AnnotationAssertion(rdfs:label "EC 3.5.1.4 (amidase) inhibitor") +SubClassOf( ) + +# Class: (food component) + +AnnotationAssertion( "A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.") +AnnotationAssertion( "CHEBI:78295") +AnnotationAssertion(rdfs:label "food component") +SubClassOf( ) + +# Class: (environmental contaminant) + +AnnotationAssertion( "Any minor or unwanted substance introduced into the environment that can have undesired effects.") +AnnotationAssertion( "CHEBI:78298") +AnnotationAssertion(rdfs:label "environmental contaminant") +SubClassOf( ) + +# Class: (refrigerant) + +AnnotationAssertion( "A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a \"R\" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.") +AnnotationAssertion( "CHEBI:78433") +AnnotationAssertion(rdfs:label "refrigerant") +SubClassOf( ) + +# Class: (alpha-amino-acid zwitterion) + +AnnotationAssertion( "An amino acid-zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.") +AnnotationAssertion( "CHEBI:78608") +AnnotationAssertion(rdfs:label "alpha-amino-acid zwitterion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrates and carbohydrate derivatives) + +AnnotationAssertion( "Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.") +AnnotationAssertion( "CHEBI:78616") +AnnotationAssertion(rdfs:label "carbohydrates and carbohydrate derivatives") +SubClassOf( ) + +# Class: (fundamental metabolite) + +AnnotationAssertion( "Any metabolite produced by all living cells.") +AnnotationAssertion( "CHEBI:78675") +AnnotationAssertion(rdfs:label "fundamental metabolite") +SubClassOf( ) + +# Class: (trivalent inorganic anion) + +AnnotationAssertion( "Any inorganic anion with a valency of three.") +AnnotationAssertion( "CHEBI:79387") +AnnotationAssertion(rdfs:label "trivalent inorganic anion") +SubClassOf( ) + +# Class: (divalent inorganic anion) + +AnnotationAssertion( "Any inorganic anion with a valency of two.") +AnnotationAssertion( "CHEBI:79388") +AnnotationAssertion(rdfs:label "divalent inorganic anion") +SubClassOf( ) + +# Class: (monovalent inorganic anion) + +AnnotationAssertion( "Any inorganic anion with a valency of one.") +AnnotationAssertion( "CHEBI:79389") +AnnotationAssertion(rdfs:label "monovalent inorganic anion") +SubClassOf( ) + +# Class: (aliphatic nitrile) + +AnnotationAssertion( "Any nitrile derived from an aliphatic compound.") +AnnotationAssertion( "CHEBI:80291") +AnnotationAssertion(rdfs:label "aliphatic nitrile") +SubClassOf( ) +SubClassOf( ) + +# Class: (crustacean metabolite) + +AnnotationAssertion( "An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill.") +AnnotationAssertion( "CHEBI:83039") +AnnotationAssertion(rdfs:label "crustacean metabolite") +SubClassOf( ) + +# Class: (Daphnia magna metabolite) + +AnnotationAssertion( "A Daphnia metabolite produced by the species Daphnia magna.") +AnnotationAssertion( "CHEBI:83056") +AnnotationAssertion(rdfs:label "Daphnia magna metabolite") +SubClassOf( ) + +# Class: (Daphnia metabolite) + +AnnotationAssertion( "A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia") +AnnotationAssertion( "CHEBI:83057") +AnnotationAssertion(rdfs:label "Daphnia metabolite") +SubClassOf( ) + +# Class: (proteinogenic amino acid derivative) + +AnnotationAssertion( "Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom.") +AnnotationAssertion( "CHEBI:83811") +AnnotationAssertion(rdfs:label "proteinogenic amino acid derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (proteinogenic amino acid) + +AnnotationAssertion( "Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration.") +AnnotationAssertion( "CHEBI:83813") +AnnotationAssertion(rdfs:label "proteinogenic amino acid") +SubClassOf( ) + +# Class: (amino-acid derivative) + +AnnotationAssertion( "Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues.") +AnnotationAssertion( "CHEBI:83821") +AnnotationAssertion(rdfs:label "amino-acid derivative") +SubClassOf( ) + +# Class: (pentose phosphate) + +AnnotationAssertion( "Any phospho sugar that is the phosphate derivative of pentose.") +AnnotationAssertion( "CHEBI:84055") +AnnotationAssertion(rdfs:label "pentose phosphate") +SubClassOf( ) +SubClassOf( ) + +# Class: (algal metabolite) + +AnnotationAssertion( "Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.") +AnnotationAssertion( "CHEBI:84735") +AnnotationAssertion(rdfs:label "algal metabolite") +SubClassOf( ) + +# Class: (antifungal agrochemical) + +AnnotationAssertion( "Any substance used in acriculture, horticulture, forestry, etc. for its fungicidal properties.") +AnnotationAssertion( "CHEBI:86328") +AnnotationAssertion(rdfs:label "antifungal agrochemical") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (aromatic fungicide) + +AnnotationAssertion( "An organic aromatic compound that has been used as a fungicide.") +AnnotationAssertion( "CHEBI:87034") +AnnotationAssertion(rdfs:label "aromatic fungicide") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (spectroscopy) + +AnnotationAssertion( "CHMO:0000228") +AnnotationAssertion(rdfs:label "spectroscopy") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mass spectrometry) + +AnnotationAssertion( "CHMO:0000470") +AnnotationAssertion(rdfs:label "mass spectrometry") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gas chromatography-mass spectrometry) + +AnnotationAssertion( "CHMO:0000497") +AnnotationAssertion(rdfs:label "gas chromatography-mass spectrometry") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (isotope ratio mass spectrometry) + +AnnotationAssertion( "CHMO:0000506") +AnnotationAssertion(rdfs:label "isotope ratio mass spectrometry") +SubClassOf( ) + +# Class: (gas chromatography-isotope ratio mass spectrometry) + +AnnotationAssertion( "CHMO:0000508") +AnnotationAssertion(rdfs:label "gas chromatography-isotope ratio mass spectrometry") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (liquid chromatography-isotope ratio mass spectrometry) + +AnnotationAssertion( "CHMO:0000509") +AnnotationAssertion(rdfs:label "liquid chromatography-isotope ratio mass spectrometry") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (stable isotope ratio mass spectrometry) + +AnnotationAssertion( "CHMO:0000514") +AnnotationAssertion(rdfs:label "stable isotope ratio mass spectrometry") +SubClassOf( ) + +# Class: (liquid chromatography-mass spectrometry) + +AnnotationAssertion( "CHMO:0000524") +AnnotationAssertion(rdfs:label "liquid chromatography-mass spectrometry") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (selective ion monitoring) + +AnnotationAssertion( "CHMO:0000571") +AnnotationAssertion(rdfs:label "selective ion monitoring") +SubClassOf( ) + +# Class: (tandem mass spectrometry) + +AnnotationAssertion( "CHMO:0000575") +AnnotationAssertion(rdfs:label "tandem mass spectrometry") +SubClassOf( ) + +# Class: (nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000591") +AnnotationAssertion(rdfs:label "nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (one-dimensional nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000592") +AnnotationAssertion(rdfs:label "one-dimensional nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (1H nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000593") +AnnotationAssertion(rdfs:label "1H nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (13C nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000595") +AnnotationAssertion(rdfs:label "13C nuclear magnetic resonance spectroscopy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (19F nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000597") +AnnotationAssertion(rdfs:label "19F nuclear magnetic resonance spectroscopy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (two-dimensional nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000598") +AnnotationAssertion(rdfs:label "two-dimensional nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (correlation spectroscopy) + +AnnotationAssertion( "CHMO:0000599") +AnnotationAssertion(rdfs:label "correlation spectroscopy") +SubClassOf( ) + +# Class: (heteronuclear correlation spectroscopy) + +AnnotationAssertion( "CHMO:0000600") +AnnotationAssertion(rdfs:label "heteronuclear correlation spectroscopy") +SubClassOf( ) + +# Class: (total correlation spectroscopy) + +AnnotationAssertion( "CHMO:0000605") +AnnotationAssertion(rdfs:label "total correlation spectroscopy") +SubClassOf( ) + +# Class: (J-spectroscopy) + +AnnotationAssertion( "CHMO:0000606") +AnnotationAssertion(rdfs:label "J-spectroscopy") +SubClassOf( ) + +# Class: (nuclear Overhauser enhancement spectroscopy) + +AnnotationAssertion( "CHMO:0000607") +AnnotationAssertion(rdfs:label "nuclear Overhauser enhancement spectroscopy") +SubClassOf( ) + +# Class: (pulsed nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000613") +AnnotationAssertion(rdfs:label "pulsed nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (liquid chromatography-tandem mass spectrometry) + +AnnotationAssertion( "A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series."@en) +AnnotationAssertion( "LC-MS-MS") +AnnotationAssertion( "LC-MS/MS") +AnnotationAssertion( "LC-MS2") +AnnotationAssertion( "LC-MSMS") +AnnotationAssertion( "LC/MS/MS") +AnnotationAssertion( "LCMSMS") +AnnotationAssertion( "liquid chromatography tandem mass spectrometry") +AnnotationAssertion( "liquid chromatography tandem mass spectroscopy") +AnnotationAssertion( "liquid chromatography-tandem mass spectroscopy") +AnnotationAssertion( "CHMO") +AnnotationAssertion( "CHMO:0000701") +AnnotationAssertion(rdfs:label "liquid chromatography-tandem mass spectrometry") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Carr-Purcell-Meiboom-Gill pulse sequence) + +AnnotationAssertion( "CHMO:0000718") +AnnotationAssertion(rdfs:label "Carr-Purcell-Meiboom-Gill pulse sequence") +SubClassOf( ) + +# Class: (quadrupolar Carr-Purcell-Meiboom-Gill pulse sequence) + +AnnotationAssertion( "CHMO:0000719") +AnnotationAssertion(rdfs:label "quadrupolar Carr-Purcell-Meiboom-Gill pulse sequence") +SubClassOf( ) + +# Class: (assay output) + +AnnotationAssertion( "CHMO:0000793") +AnnotationAssertion(rdfs:label "assay output") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (spectrum) + +AnnotationAssertion( "CHMO:0000800") +AnnotationAssertion(rdfs:label "spectrum") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mass spectrum) + +AnnotationAssertion( "CHMO:0000806") +AnnotationAssertion(rdfs:label "mass spectrum") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (heteronuclear two-dimensional nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0000931") +AnnotationAssertion(rdfs:label "heteronuclear two-dimensional nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (liquid mobile phase) + +AnnotationAssertion( "CHMO:0000991") +AnnotationAssertion(rdfs:label "liquid mobile phase") +SubClassOf( ) + +# Class: (portion of material) + +AnnotationAssertion( "CHMO:0000993") +AnnotationAssertion(rdfs:label "portion of material") +SubClassOf( ) + +# Class: (chromatographic phase) + +AnnotationAssertion( "CHMO:0000994") +AnnotationAssertion(rdfs:label "chromatographic phase") +SubClassOf( ) + +# Class: (mobile phase) + +AnnotationAssertion( "CHMO:0000995") +AnnotationAssertion(rdfs:label "mobile phase") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gaseous mobile phase) + +AnnotationAssertion( "CHMO:0000996") +AnnotationAssertion(rdfs:label "gaseous mobile phase") +SubClassOf( ) + +# Class: (chromatography column) + +AnnotationAssertion( "CHMO:0000997") +AnnotationAssertion(rdfs:label "chromatography column") +SubClassOf( ) + +# Class: (separation method) + +AnnotationAssertion( "CHMO:0000999") +AnnotationAssertion(rdfs:label "separation method") +SubClassOf( ) + +# Class: (chromatography) + +AnnotationAssertion( "CHMO:0001000") +AnnotationAssertion(rdfs:label "chromatography") +SubClassOf( ) + +# Class: (column chromatography) + +AnnotationAssertion( "CHMO:0001001") +AnnotationAssertion(rdfs:label "column chromatography") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gas chromatography) + +AnnotationAssertion( "CHMO:0001002") +AnnotationAssertion(rdfs:label "gas chromatography") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (liquid chromatography) + +AnnotationAssertion( "CHMO:0001004") +AnnotationAssertion(rdfs:label "liquid chromatography") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (1H–1H correlation spectroscopy) + +AnnotationAssertion( "CHMO:0001150") +AnnotationAssertion(rdfs:label "1H–1H correlation spectroscopy") +SubClassOf( ) + +# Class: (17O nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0001189") +AnnotationAssertion(rdfs:label "17O nuclear magnetic resonance spectroscopy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Hadamard-encoded nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0001195") +AnnotationAssertion(rdfs:label "Hadamard-encoded nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (magnetic resonance method) + +AnnotationAssertion( "CHMO:0001215") +AnnotationAssertion(rdfs:label "magnetic resonance method") +SubClassOf( ) + +# Class: (extraction) + +AnnotationAssertion( "CHMO:0001577") +AnnotationAssertion(rdfs:label "extraction") +SubClassOf( ) + +# Class: (nuclear magnetic resonance method) + +AnnotationAssertion( "CHMO:0001806") +AnnotationAssertion(rdfs:label "nuclear magnetic resonance method") +SubClassOf( ) + +# Class: (nuclear magnetic resonance pulse sequence) + +AnnotationAssertion( "CHMO:0001841") +AnnotationAssertion(rdfs:label "nuclear magnetic resonance pulse sequence") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (radio frequency pulse) + +AnnotationAssertion( "CHMO:0001842") +AnnotationAssertion(rdfs:label "radio frequency pulse") +SubClassOf( ) + +# Class: (decoupling pulse sequence) + +AnnotationAssertion( "CHMO:0001844") +AnnotationAssertion(rdfs:label "decoupling pulse sequence") +SubClassOf( ) + +# Class: (magic angle spinning decoupling pulse sequence) + +AnnotationAssertion( "CHMO:0001852") +AnnotationAssertion(rdfs:label "magic angle spinning decoupling pulse sequence") +SubClassOf( ) + +# Class: (flip flop spectroscopy) + +AnnotationAssertion( "CHMO:0001862") +AnnotationAssertion(rdfs:label "flip flop spectroscopy") +SubClassOf( ) + +# Class: (heteronuclear Hartmann Hahn pulse sequence) + +AnnotationAssertion( "CHMO:0001863") +AnnotationAssertion(rdfs:label "heteronuclear Hartmann Hahn pulse sequence") +SubClassOf( ) + +# Class: (solvent suppression pulse sequence) + +AnnotationAssertion( "CHMO:0001864") +AnnotationAssertion(rdfs:label "solvent suppression pulse sequence") +SubClassOf( ) + +# Class: (jump and return pulse sequence) + +AnnotationAssertion( "CHMO:0001865") +AnnotationAssertion(rdfs:label "jump and return pulse sequence") +SubClassOf( ) + +# Class: (water elimination Fourier transform) + +AnnotationAssertion( "CHMO:0001866") +AnnotationAssertion(rdfs:label "water elimination Fourier transform") +SubClassOf( ) + +# Class: (water suppression through gradient tailored excitation) + +AnnotationAssertion( "CHMO:0001867") +AnnotationAssertion(rdfs:label "water suppression through gradient tailored excitation") +SubClassOf( ) + +# Class: (spin echo pulse sequence) + +AnnotationAssertion( "CHMO:0001868") +AnnotationAssertion(rdfs:label "spin echo pulse sequence") +SubClassOf( ) + +# Class: (total suppression of sidebands pulse sequence) + +AnnotationAssertion( "CHMO:0001869") +AnnotationAssertion(rdfs:label "total suppression of sidebands pulse sequence") +SubClassOf( ) + +# Class: (two-dimensional heteronuclear single quantum coherence-nuclear Overhauser effect spectroscopy) + +AnnotationAssertion( "CHMO:0002060") +AnnotationAssertion(rdfs:label "two-dimensional heteronuclear single quantum coherence-nuclear Overhauser effect spectroscopy") +SubClassOf( ) + +# Class: (13C–13C correlation spectroscopy) + +AnnotationAssertion( "CHMO:0002301") +AnnotationAssertion(rdfs:label "13C–13C correlation spectroscopy") +SubClassOf( ) + +# Class: (1H–13C heteronuclear correlation spectroscopy) + +AnnotationAssertion( "CHMO:0002380") +AnnotationAssertion(rdfs:label "1H–13C heteronuclear correlation spectroscopy") +SubClassOf( ) + +# Class: (one-dimensional 1H nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0002442") +AnnotationAssertion(rdfs:label "one-dimensional 1H nuclear magnetic resonance spectroscopy") +SubClassOf( ) + +# Class: (polymer preparation method) + +AnnotationAssertion( "CHMO:0002548") +AnnotationAssertion(rdfs:label "polymer preparation method") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (liquid chromatography nuclear magnetic resonance spectroscopy) + +AnnotationAssertion( "CHMO:0002708") +AnnotationAssertion(rdfs:label "liquid chromatography nuclear magnetic resonance spectroscopy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (elution) + +AnnotationAssertion( "CHMO:0002742") +AnnotationAssertion(rdfs:label "elution") +SubClassOf( ) + +# Class: (selected reaction monitoring) + +AnnotationAssertion( "CHMO:0002867") +AnnotationAssertion(rdfs:label "selected reaction monitoring") +SubClassOf( ) + +# Class: (cell) + +AnnotationAssertion( "PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. \"...Epithelial cells were harvested from histologically confirmed adenocarcinomas ..\""@en) +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (cultured cell) + +AnnotationAssertion(rdfs:label "cultured cell") +SubClassOf( ) +SubClassOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) + +# Class: (stem cell) + +AnnotationAssertion(rdfs:label "stem cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (single fate stem cell) + +AnnotationAssertion(rdfs:label "single fate stem cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic stem cell) + +AnnotationAssertion(rdfs:label "hematopoietic stem cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (multi fate stem cell) + +AnnotationAssertion(rdfs:label "multi fate stem cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (common lymphoid progenitor) + +AnnotationAssertion(rdfs:label "common lymphoid progenitor") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mesenchymal stem cell) + +AnnotationAssertion(rdfs:label "mesenchymal stem cell") +SubClassOf( ) +SubClassOf( ) + +# Class: (motile cell) + +AnnotationAssertion(rdfs:label "motile cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (single nucleate cell) + +AnnotationAssertion(rdfs:label "single nucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B cell) + +AnnotationAssertion(rdfs:label "B cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (eukaryotic cell) + +AnnotationAssertion(rdfs:label "eukaryotic cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Eumycetozoan cell) + +AnnotationAssertion(rdfs:label "Eumycetozoan cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (fungal cell) + +AnnotationAssertion(rdfs:label "fungal cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte) + +AnnotationAssertion(rdfs:label "lymphocyte") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (angioblastic mesenchymal cell) + +AnnotationAssertion(rdfs:label "angioblastic mesenchymal cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (experimentally modified cell in vitro) + +AnnotationAssertion(rdfs:label "experimentally modified cell in vitro") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic stem cell) + +AnnotationAssertion(rdfs:label "somatic stem cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (leukocyte) + +AnnotationAssertion(rdfs:label "leukocyte") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pro-B cell) + +AnnotationAssertion(rdfs:label "pro-B cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic multipotent progenitor cell) + +AnnotationAssertion(rdfs:label "hematopoietic multipotent progenitor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (lymphoid lineage restricted progenitor cell) + +AnnotationAssertion(rdfs:label "lymphoid lineage restricted progenitor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mononuclear leukocyte) + +AnnotationAssertion(rdfs:label "mononuclear leukocyte") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (lymphocyte of B lineage) + +AnnotationAssertion(rdfs:label "lymphocyte of B lineage") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic cell) + +AnnotationAssertion(rdfs:label "hematopoietic cell") +SubClassOf( ) + +# Class: (cell in vitro) + +AnnotationAssertion(rdfs:label "cell in vitro") +SubClassOf( ) + +# Class: (hematopoietic oligopotent progenitor cell, lineage-negative) + +AnnotationAssertion(rdfs:label "hematopoietic oligopotent progenitor cell, lineage-negative") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte of B lineage, CD19-positive) + +AnnotationAssertion(rdfs:label "lymphocyte of B lineage, CD19-positive") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B cell, CD19-positive) + +AnnotationAssertion(rdfs:label "B cell, CD19-positive") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (hematopoietic lineage restricted progenitor cell) + +AnnotationAssertion(rdfs:label "hematopoietic lineage restricted progenitor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (hematopoietic oligopotent progenitor cell) + +AnnotationAssertion(rdfs:label "hematopoietic oligopotent progenitor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleate cell) + +AnnotationAssertion(rdfs:label "nucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (connective tissue cell) + +AnnotationAssertion(rdfs:label "connective tissue cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic precursor cell) + +AnnotationAssertion(rdfs:label "hematopoietic precursor cell") +SubClassOf( ) + +# Class: (progenitor cell) + +AnnotationAssertion(rdfs:label "progenitor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (precursor cell) + +AnnotationAssertion(rdfs:label "precursor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (neutrophillic cytoplasm) + +AnnotationAssertion(rdfs:label "neutrophillic cytoplasm") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data use permission) + +AnnotationAssertion( "A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used."@en) +AnnotationAssertion( "consent code") +AnnotationAssertion( "DUO:0000001") +AnnotationAssertion(rdfs:label "data use permission"@en) +SubClassOf( ) + +# Class: (obsolete consent code primary category) + +AnnotationAssertion( "A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.") +AnnotationAssertion( "DUO:0000002") +AnnotationAssertion(rdfs:label "obsolete consent code primary category") +SubClassOf( ) + +# Class: (obsolete consent code secondary category) + +AnnotationAssertion( "A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.") +AnnotationAssertion( "DUO:0000003") +AnnotationAssertion(rdfs:label "obsolete consent code secondary category") +SubClassOf( ) + +# Class: (no restriction) + +AnnotationAssertion( "This data use permission indicates there is no restriction on use."@en) +AnnotationAssertion( "DUO:0000004") +AnnotationAssertion( "NRES") +AnnotationAssertion(rdfs:label "no restriction"@en) +SubClassOf( ) + +# Class: (obsolete general research use and clinical care) + +AnnotationAssertion( "This data use limitation indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry."@en) +AnnotationAssertion( "DUO:0000005") +AnnotationAssertion( "GRU-CC") +AnnotationAssertion(rdfs:label "obsolete general research use and clinical care"@en) +SubClassOf( ) + +# Class: (health or medical or biomedical research) + +AnnotationAssertion( "This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry."@en) +AnnotationAssertion( "DUO:0000006") +AnnotationAssertion( "HMB") +AnnotationAssertion(rdfs:label "health or medical or biomedical research"@en) +SubClassOf( ) + +# Class: (disease specific research) + +AnnotationAssertion( "This data use permission indicates that use is allowed provided it is related to the specified disease."@en) +AnnotationAssertion( "DUO:0000007") +AnnotationAssertion( "DS") +AnnotationAssertion(rdfs:label "disease specific research"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (population origins or ancestry research only) + +AnnotationAssertion( "This data use permission indicates that use of the data is limited to the study of population origins or ancestry."@en) +AnnotationAssertion( "population origins/ancestry research") +AnnotationAssertion( "DUO:0000011") +AnnotationAssertion( "POA") +AnnotationAssertion(rdfs:label "population origins or ancestry research only"@en) +SubClassOf( ) + +# Class: (research specific restrictions) + +AnnotationAssertion( "This data use modifier indicates that use is limited to studies of a certain research type."@en) +AnnotationAssertion( "DUO:0000012") +AnnotationAssertion( "RS") +AnnotationAssertion(rdfs:label "research specific restrictions"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (obsolete research use only) + +AnnotationAssertion( "This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care)."@en) +AnnotationAssertion( "DUO:0000014") +AnnotationAssertion( "RU") +AnnotationAssertion(rdfs:label "obsolete research use only"@en) +SubClassOf( ) + +# Class: (no general methods research) + +AnnotationAssertion( "This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms)."@en) +AnnotationAssertion( "DUO:0000015") +AnnotationAssertion( "NMDS") +AnnotationAssertion(rdfs:label "no general methods research"@en) +SubClassOf( ) + +# Class: (genetic studies only) + +AnnotationAssertion( "This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)"@en) +AnnotationAssertion( "DUO:0000016") +AnnotationAssertion( "GSO") +AnnotationAssertion(rdfs:label "genetic studies only"@en) +SubClassOf( ) + +# Class: (data use modifier) + +AnnotationAssertion( "Data use modifiers indicate additional conditions for use."@en) +AnnotationAssertion( "DUO:0000017") +AnnotationAssertion(rdfs:label "data use modifier"@en) +SubClassOf( ) + +# Class: (not for profit, non commercial use only) + +AnnotationAssertion( "This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use."@en) +AnnotationAssertion( "DUO:0000018") +AnnotationAssertion( "NPUNCU") +AnnotationAssertion(rdfs:label "not for profit, non commercial use only"@en) +SubClassOf( ) + +# Class: (publication required) + +AnnotationAssertion( "This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community."@en) +AnnotationAssertion( "DUO:0000019") +AnnotationAssertion( "PUB") +AnnotationAssertion(rdfs:label "publication required"@en) +SubClassOf( ) + +# Class: (collaboration required) + +AnnotationAssertion( "This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s)."@en) +AnnotationAssertion( "DUO:0000020") +AnnotationAssertion( "COL") +AnnotationAssertion(rdfs:label "collaboration required"@en) +SubClassOf( ) + +# Class: (ethics approval required) + +AnnotationAssertion( "This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval."@en) +AnnotationAssertion( "DUO:0000021") +AnnotationAssertion( "IRB") +AnnotationAssertion(rdfs:label "ethics approval required"@en) +SubClassOf( ) + +# Class: (geographical restriction) + +AnnotationAssertion( "This data use modifier indicates that use is limited to within a specific geographic region."@en) +AnnotationAssertion( "DUO:0000022") +AnnotationAssertion( "GS") +AnnotationAssertion(rdfs:label "geographical restriction"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (publication moratorium) + +AnnotationAssertion( "This data use modifier indicates that requestor agrees not to publish results of studies until a specific date."@en) +AnnotationAssertion( "publication embargo"@en) +AnnotationAssertion( "DUO:0000024") +AnnotationAssertion( "MOR") +AnnotationAssertion(rdfs:label "publication moratorium"@en) +SubClassOf( ) + +# Class: (time limit on use) + +AnnotationAssertion( "This data use modifier indicates that use is approved for a specific number of months."@en) +AnnotationAssertion( "DUO:0000025") +AnnotationAssertion( "TS") +AnnotationAssertion(rdfs:label "time limit on use"@en) +SubClassOf( ) + +# Class: (user specific restriction) + +AnnotationAssertion( "This data use modifier indicates that use is limited to use by approved users."@en) +AnnotationAssertion( "DUO:0000026") +AnnotationAssertion( "US") +AnnotationAssertion(rdfs:label "user specific restriction"@en) +SubClassOf( ) + +# Class: (project specific restriction) + +AnnotationAssertion( "This data use modifier indicates that use is limited to use within an approved project."@en) +AnnotationAssertion( "DUO:0000027") +AnnotationAssertion( "PS") +AnnotationAssertion(rdfs:label "project specific restriction"@en) +SubClassOf( ) + +# Class: (institution specific restriction) + +AnnotationAssertion( "This data use modifier indicates that use is limited to use within an approved institution."@en) +AnnotationAssertion( "DUO:0000028") +AnnotationAssertion( "IS") +AnnotationAssertion(rdfs:label "institution specific restriction"@en) +SubClassOf( ) + +# Class: (return to database or resource) + +AnnotationAssertion( "This data use modifier indicates that the requestor must return derived/enriched data to the database/resource."@en) +AnnotationAssertion( "DUO:0000029") +AnnotationAssertion( "RTN") +AnnotationAssertion(rdfs:label "return to database or resource"@en) +SubClassOf( ) + +# Class: (general research use) + +AnnotationAssertion( "This data use permission indicates that use is allowed for general research use for any research purpose."@en) +AnnotationAssertion( "DUO:0000042") +AnnotationAssertion( "GRU") +AnnotationAssertion(rdfs:label "general research use"@en) +SubClassOf( ) + +# Class: (substance with biological role role) + +AnnotationAssertion(rdfs:label "substance with biological role role") +SubClassOf( ) +SubClassOf( ) + +# Class: (substance with insecticide role) + +AnnotationAssertion(rdfs:label "substance with insecticide role") +SubClassOf( ) + +# Class: (substance with metabolite role) + +AnnotationAssertion(rdfs:label "substance with metabolite role") +SubClassOf( ) + +# Class: (substance with pesticide role) + +AnnotationAssertion(rdfs:label "substance with pesticide role") +SubClassOf( ) + +# Class: (substance with toxin role) + +AnnotationAssertion(rdfs:label "substance with toxin role") +SubClassOf( ) +SubClassOf( ) + +# Class: (substance with micronutrient role) + +AnnotationAssertion(rdfs:label "substance with micronutrient role") +SubClassOf( ) + +# Class: (substance with water-soluble vitamin (role) role) + +AnnotationAssertion(rdfs:label "substance with water-soluble vitamin (role) role") +SubClassOf( ) + +# Class: (substance with vitamin (role) role) + +AnnotationAssertion(rdfs:label "substance with vitamin (role) role") +SubClassOf( ) +SubClassOf( ) + +# Class: (substance with application role) + +AnnotationAssertion(rdfs:label "substance with application role") +SubClassOf( ) +SubClassOf( ) + +# Class: (substance with nutrient role) + +AnnotationAssertion(rdfs:label "substance with nutrient role") +SubClassOf( ) + +# Class: (substance with xenobiotic role) + +AnnotationAssertion(rdfs:label "substance with xenobiotic role") +SubClassOf( ) + +# Class: (substance with acid role) + +AnnotationAssertion(rdfs:label "substance with acid role") +SubClassOf( ) + +# Class: (substance with role role) + +AnnotationAssertion(rdfs:label "substance with role role") + +# Class: (substance with chemical role role) + +AnnotationAssertion(rdfs:label "substance with chemical role role") +SubClassOf( ) +SubClassOf( ) + +# Class: (substance with biochemical role role) + +AnnotationAssertion(rdfs:label "substance with biochemical role role") +SubClassOf( ) + +# Class: (substance with physiological role role) + +AnnotationAssertion(rdfs:label "substance with physiological role role") +SubClassOf( ) + +# Class: (substance with poison role) + +AnnotationAssertion(rdfs:label "substance with poison role") +SubClassOf( ) + +# Class: (substance with food component role) + +AnnotationAssertion(rdfs:label "substance with food component role") +SubClassOf( ) + +# Class: (regulation of DNA recombination) + +AnnotationAssertion( "GO:0000018") +AnnotationAssertion(rdfs:label "regulation of DNA recombination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (peptidyltransferase activity) + +AnnotationAssertion( "GO:0000048") +AnnotationAssertion(rdfs:label "peptidyltransferase activity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (urea cycle) + +AnnotationAssertion( "GO:0000050") +AnnotationAssertion(rdfs:label "urea cycle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear chromosome) + +AnnotationAssertion( "GO:0000228") +AnnotationAssertion(rdfs:label "nuclear chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial chromosome) + +AnnotationAssertion( "GO:0000262") +AnnotationAssertion(rdfs:label "mitochondrial chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromatin) + +AnnotationAssertion( "GO:0000785") +AnnotationAssertion(rdfs:label "chromatin") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (heterochromatin) + +AnnotationAssertion( "GO:0000792") +AnnotationAssertion(rdfs:label "heterochromatin") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sex chromosome) + +AnnotationAssertion( "GO:0000803") +AnnotationAssertion(rdfs:label "sex chromosome") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell morphogenesis) + +AnnotationAssertion( "GO:0000902") +AnnotationAssertion(rdfs:label "cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to acid chemical) + +AnnotationAssertion( "GO:0001101") +AnnotationAssertion(rdfs:label "response to acid chemical") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (RNA-templated transcription) + +AnnotationAssertion( "GO:0001172") +AnnotationAssertion(rdfs:label "RNA-templated transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (angiogenesis) + +AnnotationAssertion( "GO:0001525") +AnnotationAssertion(rdfs:label "angiogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (blood vessel development) + +AnnotationAssertion( "GO:0001568") +AnnotationAssertion(rdfs:label "blood vessel development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vasculogenesis) + +AnnotationAssertion( "GO:0001570") +AnnotationAssertion(rdfs:label "vasculogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ameboidal-type cell migration) + +AnnotationAssertion( "GO:0001667") +AnnotationAssertion(rdfs:label "ameboidal-type cell migration") +SubClassOf( ) + +# Class: (formation of translation initiation ternary complex) + +AnnotationAssertion( "GO:0001677") +AnnotationAssertion(rdfs:label "formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sex chromatin) + +AnnotationAssertion( "GO:0001739") +AnnotationAssertion(rdfs:label "sex chromatin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell activation) + +AnnotationAssertion( "GO:0001775") +AnnotationAssertion(rdfs:label "cell activation") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vasculature development) + +AnnotationAssertion( "GO:0001944") +AnnotationAssertion(rdfs:label "vasculature development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic diversification of immune receptors) + +AnnotationAssertion( "GO:0002200") +AnnotationAssertion(rdfs:label "somatic diversification of immune receptors") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic progenitor cell differentiation) + +AnnotationAssertion( "GO:0002244") +AnnotationAssertion(rdfs:label "hematopoietic progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (adaptive immune response) + +AnnotationAssertion( "GO:0002250") +AnnotationAssertion(rdfs:label "adaptive immune response") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (immune effector process) + +AnnotationAssertion( "GO:0002252") +AnnotationAssertion(rdfs:label "immune effector process") +SubClassOf( ) + +# Class: (cell activation involved in immune response) + +AnnotationAssertion( "GO:0002263") +AnnotationAssertion(rdfs:label "cell activation involved in immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte activation involved in immune response) + +AnnotationAssertion( "GO:0002285") +AnnotationAssertion(rdfs:label "lymphocyte activation involved in immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B cell activation involved in immune response) + +AnnotationAssertion( "GO:0002312") +AnnotationAssertion(rdfs:label "B cell activation involved in immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphoid progenitor cell differentiation) + +AnnotationAssertion( "GO:0002320") +AnnotationAssertion(rdfs:label "lymphoid progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pro-B cell differentiation) + +AnnotationAssertion( "GO:0002328") +AnnotationAssertion(rdfs:label "pro-B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (leukocyte activation involved in immune response) + +AnnotationAssertion( "GO:0002366") +AnnotationAssertion(rdfs:label "leukocyte activation involved in immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (immune system process) + +AnnotationAssertion( "GO:0002376") +AnnotationAssertion(rdfs:label "immune system process") +SubClassOf( ) + +# Class: (immunoglobulin production) + +AnnotationAssertion( "GO:0002377") +AnnotationAssertion(rdfs:label "immunoglobulin production") +SubClassOf( ) + +# Class: (production of molecular mediator of immune response) + +AnnotationAssertion( "GO:0002440") +AnnotationAssertion(rdfs:label "production of molecular mediator of immune response") +SubClassOf( ) +SubClassOf( ) + +# Class: (leukocyte mediated immunity) + +AnnotationAssertion( "GO:0002443") +AnnotationAssertion(rdfs:label "leukocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte mediated immunity) + +AnnotationAssertion( "GO:0002449") +AnnotationAssertion(rdfs:label "lymphocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains) + +AnnotationAssertion( "GO:0002460") +AnnotationAssertion(rdfs:label "adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (immune system development) + +AnnotationAssertion( "GO:0002520") +AnnotationAssertion(rdfs:label "immune system development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (leukocyte differentiation) + +AnnotationAssertion( "GO:0002521") +AnnotationAssertion(rdfs:label "leukocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic diversification of immune receptors via germline recombination within a single locus) + +AnnotationAssertion( "GO:0002562") +AnnotationAssertion(rdfs:label "somatic diversification of immune receptors via germline recombination within a single locus") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of immunoglobulin production) + +AnnotationAssertion( "GO:0002637") +AnnotationAssertion(rdfs:label "regulation of immunoglobulin production") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of immunoglobulin production) + +AnnotationAssertion( "GO:0002638") +AnnotationAssertion(rdfs:label "negative regulation of immunoglobulin production") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of immunoglobulin production) + +AnnotationAssertion( "GO:0002639") +AnnotationAssertion(rdfs:label "positive regulation of immunoglobulin production") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of immune system process) + +AnnotationAssertion( "GO:0002682") +AnnotationAssertion(rdfs:label "regulation of immune system process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of immune system process) + +AnnotationAssertion( "GO:0002683") +AnnotationAssertion(rdfs:label "negative regulation of immune system process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of immune system process) + +AnnotationAssertion( "GO:0002684") +AnnotationAssertion(rdfs:label "positive regulation of immune system process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of leukocyte activation) + +AnnotationAssertion( "GO:0002694") +AnnotationAssertion(rdfs:label "regulation of leukocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of leukocyte activation) + +AnnotationAssertion( "GO:0002695") +AnnotationAssertion(rdfs:label "negative regulation of leukocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of leukocyte activation) + +AnnotationAssertion( "GO:0002696") +AnnotationAssertion(rdfs:label "positive regulation of leukocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of immune effector process) + +AnnotationAssertion( "GO:0002697") +AnnotationAssertion(rdfs:label "regulation of immune effector process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of immune effector process) + +AnnotationAssertion( "GO:0002698") +AnnotationAssertion(rdfs:label "negative regulation of immune effector process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of immune effector process) + +AnnotationAssertion( "GO:0002699") +AnnotationAssertion(rdfs:label "positive regulation of immune effector process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of production of molecular mediator of immune response) + +AnnotationAssertion( "GO:0002700") +AnnotationAssertion(rdfs:label "regulation of production of molecular mediator of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of production of molecular mediator of immune response) + +AnnotationAssertion( "GO:0002701") +AnnotationAssertion(rdfs:label "negative regulation of production of molecular mediator of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of production of molecular mediator of immune response) + +AnnotationAssertion( "GO:0002702") +AnnotationAssertion(rdfs:label "positive regulation of production of molecular mediator of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of leukocyte mediated immunity) + +AnnotationAssertion( "GO:0002703") +AnnotationAssertion(rdfs:label "regulation of leukocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of leukocyte mediated immunity) + +AnnotationAssertion( "GO:0002704") +AnnotationAssertion(rdfs:label "negative regulation of leukocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of leukocyte mediated immunity) + +AnnotationAssertion( "GO:0002705") +AnnotationAssertion(rdfs:label "positive regulation of leukocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of lymphocyte mediated immunity) + +AnnotationAssertion( "GO:0002706") +AnnotationAssertion(rdfs:label "regulation of lymphocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lymphocyte mediated immunity) + +AnnotationAssertion( "GO:0002707") +AnnotationAssertion(rdfs:label "negative regulation of lymphocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lymphocyte mediated immunity) + +AnnotationAssertion( "GO:0002708") +AnnotationAssertion(rdfs:label "positive regulation of lymphocyte mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of B cell mediated immunity) + +AnnotationAssertion( "GO:0002712") +AnnotationAssertion(rdfs:label "regulation of B cell mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of B cell mediated immunity) + +AnnotationAssertion( "GO:0002713") +AnnotationAssertion(rdfs:label "negative regulation of B cell mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of B cell mediated immunity) + +AnnotationAssertion( "GO:0002714") +AnnotationAssertion(rdfs:label "positive regulation of B cell mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of adaptive immune response) + +AnnotationAssertion( "GO:0002819") +AnnotationAssertion(rdfs:label "regulation of adaptive immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of adaptive immune response) + +AnnotationAssertion( "GO:0002820") +AnnotationAssertion(rdfs:label "negative regulation of adaptive immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of adaptive immune response) + +AnnotationAssertion( "GO:0002821") +AnnotationAssertion(rdfs:label "positive regulation of adaptive immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains) + +AnnotationAssertion( "GO:0002822") +AnnotationAssertion(rdfs:label "regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains) + +AnnotationAssertion( "GO:0002823") +AnnotationAssertion(rdfs:label "negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains) + +AnnotationAssertion( "GO:0002824") +AnnotationAssertion(rdfs:label "positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to biotic stimulus) + +AnnotationAssertion( "GO:0002831") +AnnotationAssertion(rdfs:label "regulation of response to biotic stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to biotic stimulus) + +AnnotationAssertion( "GO:0002832") +AnnotationAssertion(rdfs:label "negative regulation of response to biotic stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to biotic stimulus) + +AnnotationAssertion( "GO:0002833") +AnnotationAssertion(rdfs:label "positive regulation of response to biotic stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (developmental process involved in reproduction) + +AnnotationAssertion( "GO:0003006") +AnnotationAssertion(rdfs:label "developmental process involved in reproduction") +EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (molecular_function) + +AnnotationAssertion( "GO:0003674") +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (catalytic activity) + +AnnotationAssertion( "GO:0003824") +AnnotationAssertion(rdfs:label "catalytic activity") +SubClassOf( ) + +# Class: (RNA-directed DNA polymerase activity) + +AnnotationAssertion( "GO:0003964") +AnnotationAssertion(rdfs:label "RNA-directed DNA polymerase activity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular_component) + +AnnotationAssertion( "GO:0005575") +AnnotationAssertion(rdfs:label "cellular_component") +SubClassOf( ) +DisjointClasses( ) +DisjointUnion( ) + +# Class: (intracellular anatomical structure) + +AnnotationAssertion( "GO:0005622") +AnnotationAssertion(rdfs:label "intracellular anatomical structure") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleus) + +AnnotationAssertion( "GO:0005634") +AnnotationAssertion(rdfs:label "nucleus") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (nuclear envelope) + +AnnotationAssertion( "GO:0005635") +AnnotationAssertion(rdfs:label "nuclear envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromatin silencing complex) + +AnnotationAssertion( "GO:0005677") +AnnotationAssertion(rdfs:label "chromatin silencing complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromosome) + +AnnotationAssertion( "GO:0005694") +AnnotationAssertion(rdfs:label "chromosome") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointUnion( ) + +# Class: (cytoplasm) + +AnnotationAssertion( "GO:0005737") +AnnotationAssertion(rdfs:label "cytoplasm") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrion) + +AnnotationAssertion( "GO:0005739") +AnnotationAssertion(rdfs:label "mitochondrion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial envelope) + +AnnotationAssertion( "GO:0005740") +AnnotationAssertion(rdfs:label "mitochondrial envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial matrix) + +AnnotationAssertion( "GO:0005759") +AnnotationAssertion(rdfs:label "mitochondrial matrix") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vacuole) + +AnnotationAssertion( "GO:0005773") +AnnotationAssertion(rdfs:label "vacuole") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vacuolar lumen) + +AnnotationAssertion( "GO:0005775") +AnnotationAssertion(rdfs:label "vacuolar lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plasma membrane) + +AnnotationAssertion( "GO:0005886") +AnnotationAssertion(rdfs:label "plasma membrane") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell cortex) + +AnnotationAssertion( "GO:0005938") +AnnotationAssertion(rdfs:label "cell cortex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate metabolic process) + +AnnotationAssertion( "GO:0005975") +AnnotationAssertion(rdfs:label "carbohydrate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monosaccharide metabolic process) + +AnnotationAssertion( "GO:0005996") +AnnotationAssertion(rdfs:label "monosaccharide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic acid metabolic process) + +AnnotationAssertion( "GO:0006082") +AnnotationAssertion(rdfs:label "organic acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (acetate metabolic process) + +AnnotationAssertion( "GO:0006083") +AnnotationAssertion(rdfs:label "acetate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (generation of precursor metabolites and energy) + +AnnotationAssertion( "GO:0006091") +AnnotationAssertion(rdfs:label "generation of precursor metabolites and energy") +SubClassOf( ) + +# Class: (regulation of carbohydrate metabolic process) + +AnnotationAssertion( "GO:0006109") +AnnotationAssertion(rdfs:label "regulation of carbohydrate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase-containing compound metabolic process) + +AnnotationAssertion( "GO:0006139") +AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nucleotide metabolic process) + +AnnotationAssertion( "GO:0006140") +AnnotationAssertion(rdfs:label "regulation of nucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA metabolic process) + +AnnotationAssertion( "GO:0006259") +AnnotationAssertion(rdfs:label "DNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (RNA-templated DNA biosynthetic process) + +AnnotationAssertion( "GO:0006278") +AnnotationAssertion(rdfs:label "RNA-templated DNA biosynthetic process") +SubClassOf( ) + +# Class: (DNA recombination) + +AnnotationAssertion( "GO:0006310") +AnnotationAssertion(rdfs:label "DNA recombination") +SubClassOf( ) + +# Class: (chromatin organization) + +AnnotationAssertion( "GO:0006325") +AnnotationAssertion(rdfs:label "chromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromatin remodeling) + +AnnotationAssertion( "GO:0006338") +AnnotationAssertion(rdfs:label "chromatin remodeling") +SubClassOf( ) + +# Class: (DNA-templated transcription) + +AnnotationAssertion( "GO:0006351") +AnnotationAssertion(rdfs:label "DNA-templated transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of DNA-templated transcription) + +AnnotationAssertion( "GO:0006355") +AnnotationAssertion(rdfs:label "regulation of DNA-templated transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tRNA metabolic process) + +AnnotationAssertion( "GO:0006399") +AnnotationAssertion(rdfs:label "tRNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translation) + +AnnotationAssertion( "GO:0006412") +AnnotationAssertion(rdfs:label "translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational initiation) + +AnnotationAssertion( "GO:0006413") +AnnotationAssertion(rdfs:label "translational initiation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational elongation) + +AnnotationAssertion( "GO:0006414") +AnnotationAssertion(rdfs:label "translational elongation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational termination) + +AnnotationAssertion( "GO:0006415") +AnnotationAssertion(rdfs:label "translational termination") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of translation) + +AnnotationAssertion( "GO:0006417") +AnnotationAssertion(rdfs:label "regulation of translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of translational initiation) + +AnnotationAssertion( "GO:0006446") +AnnotationAssertion(rdfs:label "regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of translational elongation) + +AnnotationAssertion( "GO:0006448") +AnnotationAssertion(rdfs:label "regulation of translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of translational termination) + +AnnotationAssertion( "GO:0006449") +AnnotationAssertion(rdfs:label "regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (peptide metabolic process) + +AnnotationAssertion( "GO:0006518") +AnnotationAssertion(rdfs:label "peptide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid metabolic process) + +AnnotationAssertion( "GO:0006520") +AnnotationAssertion(rdfs:label "amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of amino acid metabolic process) + +AnnotationAssertion( "GO:0006521") +AnnotationAssertion(rdfs:label "regulation of amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycine metabolic process) + +AnnotationAssertion( "GO:0006544") +AnnotationAssertion(rdfs:label "glycine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (glycine biosynthetic process) + +AnnotationAssertion( "GO:0006545") +AnnotationAssertion(rdfs:label "glycine biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (modified amino acid metabolic process) + +AnnotationAssertion( "GO:0006575") +AnnotationAssertion(rdfs:label "modified amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatine metabolic process) + +AnnotationAssertion( "GO:0006600") +AnnotationAssertion(rdfs:label "creatine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatine biosynthetic process) + +AnnotationAssertion( "GO:0006601") +AnnotationAssertion(rdfs:label "creatine biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lipid metabolic process) + +AnnotationAssertion( "GO:0006629") +AnnotationAssertion(rdfs:label "lipid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (isoprenoid metabolic process) + +AnnotationAssertion( "GO:0006720") +AnnotationAssertion(rdfs:label "isoprenoid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside phosphate metabolic process) + +AnnotationAssertion( "GO:0006753") +AnnotationAssertion(rdfs:label "nucleoside phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vitamin metabolic process) + +AnnotationAssertion( "GO:0006766") +AnnotationAssertion(rdfs:label "vitamin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biotin metabolic process) + +AnnotationAssertion( "GO:0006768") +AnnotationAssertion(rdfs:label "biotin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sulfur compound metabolic process) + +AnnotationAssertion( "GO:0006790") +AnnotationAssertion(rdfs:label "sulfur compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus metabolic process) + +AnnotationAssertion( "GO:0006793") +AnnotationAssertion(rdfs:label "phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphate-containing compound metabolic process) + +AnnotationAssertion( "GO:0006796") +AnnotationAssertion(rdfs:label "phosphate-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (xenobiotic metabolic process) + +AnnotationAssertion( "GO:0006805") +AnnotationAssertion(rdfs:label "xenobiotic metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (immune response) + +AnnotationAssertion( "GO:0006955") +AnnotationAssertion(rdfs:label "immune response") +SubClassOf( ) +SubClassOf( ) + +# Class: (organelle organization) + +AnnotationAssertion( "GO:0006996") +AnnotationAssertion(rdfs:label "organelle organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleus organization) + +AnnotationAssertion( "GO:0006997") +AnnotationAssertion(rdfs:label "nucleus organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear envelope organization) + +AnnotationAssertion( "GO:0006998") +AnnotationAssertion(rdfs:label "nuclear envelope organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrion organization) + +AnnotationAssertion( "GO:0007005") +AnnotationAssertion(rdfs:label "mitochondrion organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plasma membrane organization) + +AnnotationAssertion( "GO:0007009") +AnnotationAssertion(rdfs:label "plasma membrane organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cytoplasm organization) + +AnnotationAssertion( "GO:0007028") +AnnotationAssertion(rdfs:label "cytoplasm organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vacuole organization) + +AnnotationAssertion( "GO:0007033") +AnnotationAssertion(rdfs:label "vacuole organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (multicellular organism development) + +AnnotationAssertion( "GO:0007275") +AnnotationAssertion(rdfs:label "multicellular organism development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sex determination) + +AnnotationAssertion( "GO:0007530") +AnnotationAssertion(rdfs:label "sex determination") +SubClassOf( ) + +# Class: (response to nutrient) + +AnnotationAssertion( "GO:0007584") +AnnotationAssertion(rdfs:label "response to nutrient") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biological_process) + +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +DisjointClasses( ) + +# Class: (metabolic process) + +AnnotationAssertion( "GO:0008152") +AnnotationAssertion(rdfs:label "metabolic process") +SubClassOf( ) + +# Class: (isoprenoid biosynthetic process) + +AnnotationAssertion( "GO:0008299") +AnnotationAssertion(rdfs:label "isoprenoid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lipid biosynthetic process) + +AnnotationAssertion( "GO:0008610") +AnnotationAssertion(rdfs:label "lipid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid biosynthetic process) + +AnnotationAssertion( "GO:0008652") +AnnotationAssertion(rdfs:label "amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biosynthetic process) + +AnnotationAssertion( "GO:0009058") +AnnotationAssertion(rdfs:label "biosynthetic process") +SubClassOf( ) + +# Class: (macromolecule biosynthetic process) + +AnnotationAssertion( "GO:0009059") +AnnotationAssertion(rdfs:label "macromolecule biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anaerobic respiration) + +AnnotationAssertion( "GO:0009061") +AnnotationAssertion(rdfs:label "anaerobic respiration") +SubClassOf( ) + +# Class: (serine family amino acid biosynthetic process) + +AnnotationAssertion( "GO:0009070") +AnnotationAssertion(rdfs:label "serine family amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biotin biosynthetic process) + +AnnotationAssertion( "GO:0009102") +AnnotationAssertion(rdfs:label "biotin biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vitamin biosynthetic process) + +AnnotationAssertion( "GO:0009110") +AnnotationAssertion(rdfs:label "vitamin biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase metabolic process) + +AnnotationAssertion( "GO:0009112") +AnnotationAssertion(rdfs:label "nucleobase metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside metabolic process) + +AnnotationAssertion( "GO:0009116") +AnnotationAssertion(rdfs:label "nucleoside metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleotide metabolic process) + +AnnotationAssertion( "GO:0009117") +AnnotationAssertion(rdfs:label "nucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nucleoside metabolic process) + +AnnotationAssertion( "GO:0009118") +AnnotationAssertion(rdfs:label "regulation of nucleoside metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside biosynthetic process) + +AnnotationAssertion( "GO:0009163") +AnnotationAssertion(rdfs:label "nucleoside biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleotide biosynthetic process) + +AnnotationAssertion( "GO:0009165") +AnnotationAssertion(rdfs:label "nucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (deoxyribonucleotide metabolic process) + +AnnotationAssertion( "GO:0009262") +AnnotationAssertion(rdfs:label "deoxyribonucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (deoxyribonucleotide biosynthetic process) + +AnnotationAssertion( "GO:0009263") +AnnotationAssertion(rdfs:label "deoxyribonucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleotide biosynthetic process) + +AnnotationAssertion( "GO:0009265") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoid) + +AnnotationAssertion( "GO:0009295") +AnnotationAssertion(rdfs:label "nucleoid") +SubClassOf( ) + +# Class: (tRNA transcription) + +AnnotationAssertion( "GO:0009304") +AnnotationAssertion(rdfs:label "tRNA transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amine metabolic process) + +AnnotationAssertion( "GO:0009308") +AnnotationAssertion(rdfs:label "amine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amine biosynthetic process) + +AnnotationAssertion( "GO:0009309") +AnnotationAssertion(rdfs:label "amine biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (2'-deoxyribonucleotide metabolic process) + +AnnotationAssertion( "GO:0009394") +AnnotationAssertion(rdfs:label "2'-deoxyribonucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (toxin biosynthetic process) + +AnnotationAssertion( "GO:0009403") +AnnotationAssertion(rdfs:label "toxin biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (toxin metabolic process) + +AnnotationAssertion( "GO:0009404") +AnnotationAssertion(rdfs:label "toxin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to xenobiotic stimulus) + +AnnotationAssertion( "GO:0009410") +AnnotationAssertion(rdfs:label "response to xenobiotic stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to water) + +AnnotationAssertion( "GO:0009415") +AnnotationAssertion(rdfs:label "response to water") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast) + +AnnotationAssertion( "GO:0009507") +AnnotationAssertion(rdfs:label "chloroplast") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid chromosome) + +AnnotationAssertion( "GO:0009508") +AnnotationAssertion(rdfs:label "plastid chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid envelope) + +AnnotationAssertion( "GO:0009526") +AnnotationAssertion(rdfs:label "plastid envelope") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid stroma) + +AnnotationAssertion( "GO:0009532") +AnnotationAssertion(rdfs:label "plastid stroma") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid) + +AnnotationAssertion( "GO:0009536") +AnnotationAssertion(rdfs:label "plastid") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast stroma) + +AnnotationAssertion( "GO:0009570") +AnnotationAssertion(rdfs:label "chloroplast stroma") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to external stimulus) + +AnnotationAssertion( "GO:0009605") +AnnotationAssertion(rdfs:label "response to external stimulus") +SubClassOf( ) + +# Class: (response to biotic stimulus) + +AnnotationAssertion( "GO:0009607") +AnnotationAssertion(rdfs:label "response to biotic stimulus") +SubClassOf( ) + +# Class: (response to virus) + +AnnotationAssertion( "GO:0009615") +AnnotationAssertion(rdfs:label "response to virus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to bacterium) + +AnnotationAssertion( "GO:0009617") +AnnotationAssertion(rdfs:label "response to bacterium") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to fungus) + +AnnotationAssertion( "GO:0009620") +AnnotationAssertion(rdfs:label "response to fungus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to abiotic stimulus) + +AnnotationAssertion( "GO:0009628") +AnnotationAssertion(rdfs:label "response to abiotic stimulus") +SubClassOf( ) + +# Class: (response to toxic substance) + +AnnotationAssertion( "GO:0009636") +AnnotationAssertion(rdfs:label "response to toxic substance") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure morphogenesis) + +AnnotationAssertion( "GO:0009653") +AnnotationAssertion(rdfs:label "anatomical structure morphogenesis") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (plastid organization) + +AnnotationAssertion( "GO:0009657") +AnnotationAssertion(rdfs:label "plastid organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast organization) + +AnnotationAssertion( "GO:0009658") +AnnotationAssertion(rdfs:label "chloroplast organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid membrane organization) + +AnnotationAssertion( "GO:0009668") +AnnotationAssertion(rdfs:label "plastid membrane organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to carbohydrate) + +AnnotationAssertion( "GO:0009743") +AnnotationAssertion(rdfs:label "response to carbohydrate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tissue development) + +AnnotationAssertion( "GO:0009888") +AnnotationAssertion(rdfs:label "tissue development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of biosynthetic process) + +AnnotationAssertion( "GO:0009889") +AnnotationAssertion(rdfs:label "regulation of biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of biosynthetic process) + +AnnotationAssertion( "GO:0009890") +AnnotationAssertion(rdfs:label "negative regulation of biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of biosynthetic process) + +AnnotationAssertion( "GO:0009891") +AnnotationAssertion(rdfs:label "positive regulation of biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of metabolic process) + +AnnotationAssertion( "GO:0009892") +AnnotationAssertion(rdfs:label "negative regulation of metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of metabolic process) + +AnnotationAssertion( "GO:0009893") +AnnotationAssertion(rdfs:label "positive regulation of metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular process) + +AnnotationAssertion( "GO:0009987") +AnnotationAssertion(rdfs:label "cellular process") +SubClassOf( ) + +# Class: (response to acetate) + +AnnotationAssertion( "GO:0010034") +AnnotationAssertion(rdfs:label "response to acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to metal ion) + +AnnotationAssertion( "GO:0010038") +AnnotationAssertion(rdfs:label "response to metal ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to nitrate) + +AnnotationAssertion( "GO:0010167") +AnnotationAssertion(rdfs:label "response to nitrate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (body morphogenesis) + +AnnotationAssertion( "GO:0010171") +AnnotationAssertion(rdfs:label "body morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (endomembrane system organization) + +AnnotationAssertion( "GO:0010256") +AnnotationAssertion(rdfs:label "endomembrane system organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gene expression) + +AnnotationAssertion( "GO:0010467") +AnnotationAssertion(rdfs:label "gene expression") +SubClassOf( ) + +# Class: (regulation of gene expression) + +AnnotationAssertion( "GO:0010468") +AnnotationAssertion(rdfs:label "regulation of gene expression") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of membrane disassembly) + +AnnotationAssertion( "GO:0010549") +AnnotationAssertion(rdfs:label "regulation of membrane disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of macromolecule biosynthetic process) + +AnnotationAssertion( "GO:0010556") +AnnotationAssertion(rdfs:label "regulation of macromolecule biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of macromolecule biosynthetic process) + +AnnotationAssertion( "GO:0010557") +AnnotationAssertion(rdfs:label "positive regulation of macromolecule biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of macromolecule biosynthetic process) + +AnnotationAssertion( "GO:0010558") +AnnotationAssertion(rdfs:label "negative regulation of macromolecule biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of phosphorus metabolic process) + +AnnotationAssertion( "GO:0010562") +AnnotationAssertion(rdfs:label "positive regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of phosphorus metabolic process) + +AnnotationAssertion( "GO:0010563") +AnnotationAssertion(rdfs:label "negative regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of macromolecule metabolic process) + +AnnotationAssertion( "GO:0010604") +AnnotationAssertion(rdfs:label "positive regulation of macromolecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of macromolecule metabolic process) + +AnnotationAssertion( "GO:0010605") +AnnotationAssertion(rdfs:label "negative regulation of macromolecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (post-transcriptional regulation of gene expression) + +AnnotationAssertion( "GO:0010608") +AnnotationAssertion(rdfs:label "post-transcriptional regulation of gene expression") +SubClassOf( ) + +# Class: (positive regulation of gene expression) + +AnnotationAssertion( "GO:0010628") +AnnotationAssertion(rdfs:label "positive regulation of gene expression") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of gene expression) + +AnnotationAssertion( "GO:0010629") +AnnotationAssertion(rdfs:label "negative regulation of gene expression") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of organelle organization) + +AnnotationAssertion( "GO:0010638") +AnnotationAssertion(rdfs:label "positive regulation of organelle organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of organelle organization) + +AnnotationAssertion( "GO:0010639") +AnnotationAssertion(rdfs:label "negative regulation of organelle organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell development) + +AnnotationAssertion( "GO:0010720") +AnnotationAssertion(rdfs:label "positive regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell development) + +AnnotationAssertion( "GO:0010721") +AnnotationAssertion(rdfs:label "negative regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell morphogenesis) + +AnnotationAssertion( "GO:0010770") +AnnotationAssertion(rdfs:label "positive regulation of cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell morphogenesis) + +AnnotationAssertion( "GO:0010771") +AnnotationAssertion(rdfs:label "negative regulation of cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of mitochondrion organization) + +AnnotationAssertion( "GO:0010821") +AnnotationAssertion(rdfs:label "regulation of mitochondrion organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component assembly involved in morphogenesis) + +AnnotationAssertion( "GO:0010927") +AnnotationAssertion(rdfs:label "cellular component assembly involved in morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (endomembrane system) + +AnnotationAssertion( "GO:0012505") +AnnotationAssertion(rdfs:label "endomembrane system") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to amine) + +AnnotationAssertion( "GO:0014075") +AnnotationAssertion(rdfs:label "response to amine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (methane metabolic process) + +AnnotationAssertion( "GO:0015947") +AnnotationAssertion(rdfs:label "methane metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (methanogenesis) + +AnnotationAssertion( "GO:0015948") +AnnotationAssertion(rdfs:label "methanogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (energy derivation by oxidation of reduced inorganic compounds) + +AnnotationAssertion( "GO:0015975") +AnnotationAssertion(rdfs:label "energy derivation by oxidation of reduced inorganic compounds") +SubClassOf( ) + +# Class: (energy derivation by oxidation of organic compounds) + +AnnotationAssertion( "GO:0015980") +AnnotationAssertion(rdfs:label "energy derivation by oxidation of organic compounds") +SubClassOf( ) + +# Class: (membrane) + +AnnotationAssertion( "GO:0016020") +AnnotationAssertion(rdfs:label "membrane") +SubClassOf( ) + +# Class: (cellular component organization) + +AnnotationAssertion( "GO:0016043") +AnnotationAssertion(rdfs:label "cellular component organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate biosynthetic process) + +AnnotationAssertion( "GO:0016051") +AnnotationAssertion(rdfs:label "carbohydrate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic acid biosynthetic process) + +AnnotationAssertion( "GO:0016053") +AnnotationAssertion(rdfs:label "organic acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (RNA metabolic process) + +AnnotationAssertion( "GO:0016070") +AnnotationAssertion(rdfs:label "RNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic cell DNA recombination) + +AnnotationAssertion( "GO:0016444") +AnnotationAssertion(rdfs:label "somatic cell DNA recombination") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) + +# Class: (somatic diversification of immunoglobulins) + +AnnotationAssertion( "GO:0016445") +AnnotationAssertion(rdfs:label "somatic diversification of immunoglobulins") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic recombination of immunoglobulin gene segments) + +AnnotationAssertion( "GO:0016447") +AnnotationAssertion(rdfs:label "somatic recombination of immunoglobulin gene segments") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell migration) + +AnnotationAssertion( "GO:0016477") +AnnotationAssertion(rdfs:label "cell migration") +SubClassOf( ) + +# Class: (negative regulation of angiogenesis) + +AnnotationAssertion( "GO:0016525") +AnnotationAssertion(rdfs:label "negative regulation of angiogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (transferase activity) + +AnnotationAssertion( "GO:0016740") +AnnotationAssertion(rdfs:label "transferase activity") +SubClassOf( ) + +# Class: (acyltransferase activity) + +AnnotationAssertion( "GO:0016746") +AnnotationAssertion(rdfs:label "acyltransferase activity") +SubClassOf( ) + +# Class: (aminoacyltransferase activity) + +AnnotationAssertion( "GO:0016755") +AnnotationAssertion(rdfs:label "aminoacyltransferase activity") +SubClassOf( ) + +# Class: (transferase activity, transferring phosphorus-containing groups) + +AnnotationAssertion( "GO:0016772") +AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") +SubClassOf( ) + +# Class: (nucleotidyltransferase activity) + +AnnotationAssertion( "GO:0016779") +AnnotationAssertion(rdfs:label "nucleotidyltransferase activity") +SubClassOf( ) + +# Class: (response to insecticide) + +AnnotationAssertion( "GO:0017085") +AnnotationAssertion(rdfs:label "response to insecticide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (insecticide metabolic process) + +AnnotationAssertion( "GO:0017143") +AnnotationAssertion(rdfs:label "insecticide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (stem cell division) + +AnnotationAssertion( "GO:0017145") +AnnotationAssertion(rdfs:label "stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of translation) + +AnnotationAssertion( "GO:0017148") +AnnotationAssertion(rdfs:label "negative regulation of translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of lipid metabolic process) + +AnnotationAssertion( "GO:0019216") +AnnotationAssertion(rdfs:label "regulation of lipid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nucleobase-containing compound metabolic process) + +AnnotationAssertion( "GO:0019219") +AnnotationAssertion(rdfs:label "regulation of nucleobase-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of metabolic process) + +AnnotationAssertion( "GO:0019222") +AnnotationAssertion(rdfs:label "regulation of metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pentose metabolic process) + +AnnotationAssertion( "GO:0019321") +AnnotationAssertion(rdfs:label "pentose metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pentose biosynthetic process) + +AnnotationAssertion( "GO:0019322") +AnnotationAssertion(rdfs:label "pentose biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (methanogenesis, from acetate) + +AnnotationAssertion( "GO:0019385") +AnnotationAssertion(rdfs:label "methanogenesis, from acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (acetate biosynthetic process) + +AnnotationAssertion( "GO:0019413") +AnnotationAssertion(rdfs:label "acetate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyanide metabolic process) + +AnnotationAssertion( "GO:0019499") +AnnotationAssertion(rdfs:label "cyanide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein metabolic process) + +AnnotationAssertion( "GO:0019538") +AnnotationAssertion(rdfs:label "protein metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (urea metabolic process) + +AnnotationAssertion( "GO:0019627") +AnnotationAssertion(rdfs:label "urea metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organophosphate metabolic process) + +AnnotationAssertion( "GO:0019637") +AnnotationAssertion(rdfs:label "organophosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B cell mediated immunity) + +AnnotationAssertion( "GO:0019724") +AnnotationAssertion(rdfs:label "B cell mediated immunity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of isoprenoid metabolic process) + +AnnotationAssertion( "GO:0019747") +AnnotationAssertion(rdfs:label "regulation of isoprenoid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (secondary metabolic process) + +AnnotationAssertion( "GO:0019748") +AnnotationAssertion(rdfs:label "secondary metabolic process") +SubClassOf( ) + +# Class: (carboxylic acid metabolic process) + +AnnotationAssertion( "GO:0019752") +AnnotationAssertion(rdfs:label "carboxylic acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component disassembly) + +AnnotationAssertion( "GO:0022411") +AnnotationAssertion(rdfs:label "cellular component disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (reproductive process) + +AnnotationAssertion( "GO:0022414") +AnnotationAssertion(rdfs:label "reproductive process") +SubClassOf( ) + +# Class: (regulation of anatomical structure morphogenesis) + +AnnotationAssertion( "GO:0022603") +AnnotationAssertion(rdfs:label "regulation of anatomical structure morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell morphogenesis) + +AnnotationAssertion( "GO:0022604") +AnnotationAssertion(rdfs:label "regulation of cell morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component assembly) + +AnnotationAssertion( "GO:0022607") +AnnotationAssertion(rdfs:label "cellular component assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ribonucleoprotein complex biogenesis) + +AnnotationAssertion( "GO:0022613") +AnnotationAssertion(rdfs:label "ribonucleoprotein complex biogenesis") +SubClassOf( ) + +# Class: (protein-RNA complex assembly) + +AnnotationAssertion( "GO:0022618") +AnnotationAssertion(rdfs:label "protein-RNA complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hemopoiesis) + +AnnotationAssertion( "GO:0030097") +AnnotationAssertion(rdfs:label "hemopoiesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte differentiation) + +AnnotationAssertion( "GO:0030098") +AnnotationAssertion(rdfs:label "lymphocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell differentiation) + +AnnotationAssertion( "GO:0030154") +AnnotationAssertion(rdfs:label "cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B cell differentiation) + +AnnotationAssertion( "GO:0030183") +AnnotationAssertion(rdfs:label "B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell migration) + +AnnotationAssertion( "GO:0030334") +AnnotationAssertion(rdfs:label "regulation of cell migration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell migration) + +AnnotationAssertion( "GO:0030335") +AnnotationAssertion(rdfs:label "positive regulation of cell migration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell migration) + +AnnotationAssertion( "GO:0030336") +AnnotationAssertion(rdfs:label "negative regulation of cell migration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane disassembly) + +AnnotationAssertion( "GO:0030397") +AnnotationAssertion(rdfs:label "membrane disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of vitamin metabolic process) + +AnnotationAssertion( "GO:0030656") +AnnotationAssertion(rdfs:label "regulation of vitamin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nucleotide biosynthetic process) + +AnnotationAssertion( "GO:0030808") +AnnotationAssertion(rdfs:label "regulation of nucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of nucleotide biosynthetic process) + +AnnotationAssertion( "GO:0030809") +AnnotationAssertion(rdfs:label "negative regulation of nucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of nucleotide biosynthetic process) + +AnnotationAssertion( "GO:0030810") +AnnotationAssertion(rdfs:label "positive regulation of nucleotide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (autosome) + +AnnotationAssertion( "GO:0030849") +AnnotationAssertion(rdfs:label "autosome") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organelle membrane) + +AnnotationAssertion( "GO:0031090") +AnnotationAssertion(rdfs:label "organelle membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of protein-containing complex assembly) + +AnnotationAssertion( "GO:0031333") +AnnotationAssertion(rdfs:label "negative regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein-containing complex assembly) + +AnnotationAssertion( "GO:0031334") +AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of heterochromatin formation) + +AnnotationAssertion( "GO:0031445") +AnnotationAssertion(rdfs:label "regulation of heterochromatin formation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of heterochromatin formation) + +AnnotationAssertion( "GO:0031452") +AnnotationAssertion(rdfs:label "negative regulation of heterochromatin formation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of heterochromatin formation) + +AnnotationAssertion( "GO:0031453") +AnnotationAssertion(rdfs:label "positive regulation of heterochromatin formation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (heterochromatin formation) + +AnnotationAssertion( "GO:0031507") +AnnotationAssertion(rdfs:label "heterochromatin formation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to nutrient levels) + +AnnotationAssertion( "GO:0031667") +AnnotationAssertion(rdfs:label "response to nutrient levels") +SubClassOf( ) + +# Class: (cellular response to nutrient levels) + +AnnotationAssertion( "GO:0031669") +AnnotationAssertion(rdfs:label "cellular response to nutrient levels") +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to nutrient) + +AnnotationAssertion( "GO:0031670") +AnnotationAssertion(rdfs:label "cellular response to nutrient") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (nuclear membrane) + +AnnotationAssertion( "GO:0031965") +AnnotationAssertion(rdfs:label "nuclear membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial membrane) + +AnnotationAssertion( "GO:0031966") +AnnotationAssertion(rdfs:label "mitochondrial membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organelle envelope) + +AnnotationAssertion( "GO:0031967") +AnnotationAssertion(rdfs:label "organelle envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane-enclosed lumen) + +AnnotationAssertion( "GO:0031974") +AnnotationAssertion(rdfs:label "membrane-enclosed lumen") +SubClassOf( ) + +# Class: (nuclear lumen) + +AnnotationAssertion( "GO:0031981") +AnnotationAssertion(rdfs:label "nuclear lumen") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to external stimulus) + +AnnotationAssertion( "GO:0032101") +AnnotationAssertion(rdfs:label "regulation of response to external stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to external stimulus) + +AnnotationAssertion( "GO:0032102") +AnnotationAssertion(rdfs:label "negative regulation of response to external stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to external stimulus) + +AnnotationAssertion( "GO:0032103") +AnnotationAssertion(rdfs:label "positive regulation of response to external stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to nutrient levels) + +AnnotationAssertion( "GO:0032107") +AnnotationAssertion(rdfs:label "regulation of response to nutrient levels") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to nutrient levels) + +AnnotationAssertion( "GO:0032108") +AnnotationAssertion(rdfs:label "negative regulation of response to nutrient levels") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to nutrient levels) + +AnnotationAssertion( "GO:0032109") +AnnotationAssertion(rdfs:label "positive regulation of response to nutrient levels") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (multicellular organismal process) + +AnnotationAssertion( "GO:0032501") +AnnotationAssertion(rdfs:label "multicellular organismal process") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) + +# Class: (developmental process) + +AnnotationAssertion( "GO:0032502") +AnnotationAssertion(rdfs:label "developmental process") +SubClassOf( ) + +# Class: (RNA biosynthetic process) + +AnnotationAssertion( "GO:0032774") +AnnotationAssertion(rdfs:label "RNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monocarboxylic acid metabolic process) + +AnnotationAssertion( "GO:0032787") +AnnotationAssertion(rdfs:label "monocarboxylic acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing complex disassembly) + +AnnotationAssertion( "GO:0032984") +AnnotationAssertion(rdfs:label "protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-RNA complex disassembly) + +AnnotationAssertion( "GO:0032988") +AnnotationAssertion(rdfs:label "protein-RNA complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular anatomical entity morphogenesis) + +AnnotationAssertion( "GO:0032989") +AnnotationAssertion(rdfs:label "cellular anatomical entity morphogenesis") +SubClassOf( ) + +# Class: (protein-containing complex) + +AnnotationAssertion( "A ribosome is a protein complex.") +AnnotationAssertion( "protein complex") +AnnotationAssertion( "GO:0032991") +AnnotationAssertion(rdfs:label "protein-containing complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (regulation of organelle organization) + +AnnotationAssertion( "GO:0033043") +AnnotationAssertion(rdfs:label "regulation of organelle organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of chromosome organization) + +AnnotationAssertion( "GO:0033044") +AnnotationAssertion(rdfs:label "regulation of chromosome organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (V(D)J recombination) + +AnnotationAssertion( "GO:0033151") +AnnotationAssertion(rdfs:label "V(D)J recombination") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (immunoglobulin V(D)J recombination) + +AnnotationAssertion( "GO:0033152") +AnnotationAssertion(rdfs:label "immunoglobulin V(D)J recombination") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of amine metabolic process) + +AnnotationAssertion( "GO:0033238") +AnnotationAssertion(rdfs:label "regulation of amine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of amine metabolic process) + +AnnotationAssertion( "GO:0033239") +AnnotationAssertion(rdfs:label "negative regulation of amine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of amine metabolic process) + +AnnotationAssertion( "GO:0033240") +AnnotationAssertion(rdfs:label "positive regulation of amine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to vitamin) + +AnnotationAssertion( "GO:0033273") +AnnotationAssertion(rdfs:label "response to vitamin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (heterochromatin boundary formation) + +AnnotationAssertion( "GO:0033696") +AnnotationAssertion(rdfs:label "heterochromatin boundary formation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to lipid) + +AnnotationAssertion( "GO:0033993") +AnnotationAssertion(rdfs:label "response to lipid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA polymerase activity) + +AnnotationAssertion( "GO:0034061") +AnnotationAssertion(rdfs:label "DNA polymerase activity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of amide metabolic process) + +AnnotationAssertion( "GO:0034248") +AnnotationAssertion(rdfs:label "regulation of amide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of amide metabolic process) + +AnnotationAssertion( "GO:0034249") +AnnotationAssertion(rdfs:label "negative regulation of amide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of amide metabolic process) + +AnnotationAssertion( "GO:0034250") +AnnotationAssertion(rdfs:label "positive regulation of amide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to monosaccharide) + +AnnotationAssertion( "GO:0034284") +AnnotationAssertion(rdfs:label "response to monosaccharide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase-containing small molecule biosynthetic process) + +AnnotationAssertion( "GO:0034404") +AnnotationAssertion(rdfs:label "nucleobase-containing small molecule biosynthetic process") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (nucleobase-containing compound biosynthetic process) + +AnnotationAssertion( "GO:0034654") +AnnotationAssertion(rdfs:label "nucleobase-containing compound biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tube formation) + +AnnotationAssertion( "GO:0035148") +AnnotationAssertion(rdfs:label "tube formation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tube morphogenesis) + +AnnotationAssertion( "GO:0035239") +AnnotationAssertion(rdfs:label "tube morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tube development) + +AnnotationAssertion( "GO:0035295") +AnnotationAssertion(rdfs:label "tube development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell migration involved in vasculogenesis) + +AnnotationAssertion( "GO:0035441") +AnnotationAssertion(rdfs:label "cell migration involved in vasculogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (angioblast cell differentiation) + +AnnotationAssertion( "GO:0035779") +AnnotationAssertion(rdfs:label "angioblast cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (locomotion) + +AnnotationAssertion( "GO:0040011") +AnnotationAssertion(rdfs:label "locomotion") +SubClassOf( ) + +# Class: (regulation of locomotion) + +AnnotationAssertion( "GO:0040012") +AnnotationAssertion(rdfs:label "regulation of locomotion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of locomotion) + +AnnotationAssertion( "GO:0040013") +AnnotationAssertion(rdfs:label "negative regulation of locomotion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of locomotion) + +AnnotationAssertion( "GO:0040017") +AnnotationAssertion(rdfs:label "positive regulation of locomotion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (epigenetic regulation of gene expression) + +AnnotationAssertion( "GO:0040029") +AnnotationAssertion(rdfs:label "epigenetic regulation of gene expression") +SubClassOf( ) +SubClassOf( ) + +# Class: (B cell activation) + +AnnotationAssertion( "GO:0042113") +AnnotationAssertion(rdfs:label "B cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrate metabolic process) + +AnnotationAssertion( "GO:0042126") +AnnotationAssertion(rdfs:label "nitrate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid membrane) + +AnnotationAssertion( "GO:0042170") +AnnotationAssertion(rdfs:label "plastid membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (halogenated hydrocarbon metabolic process) + +AnnotationAssertion( "GO:0042197") +AnnotationAssertion(rdfs:label "halogenated hydrocarbon metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to chemical) + +AnnotationAssertion( "GO:0042221") +AnnotationAssertion(rdfs:label "response to chemical") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (water-soluble vitamin biosynthetic process) + +AnnotationAssertion( "GO:0042364") +AnnotationAssertion(rdfs:label "water-soluble vitamin biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (modified amino acid biosynthetic process) + +AnnotationAssertion( "GO:0042398") +AnnotationAssertion(rdfs:label "modified amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (benzene-containing compound metabolic process) + +AnnotationAssertion( "GO:0042537") +AnnotationAssertion(rdfs:label "benzene-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast nucleoid) + +AnnotationAssertion( "GO:0042644") +AnnotationAssertion(rdfs:label "chloroplast nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial nucleoid) + +AnnotationAssertion( "GO:0042645") +AnnotationAssertion(rdfs:label "mitochondrial nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid nucleoid) + +AnnotationAssertion( "GO:0042646") +AnnotationAssertion(rdfs:label "plastid nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast chromosome) + +AnnotationAssertion( "GO:0042648") +AnnotationAssertion(rdfs:label "chloroplast chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of sulfur metabolic process) + +AnnotationAssertion( "GO:0042762") +AnnotationAssertion(rdfs:label "regulation of sulfur metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid activation) + +AnnotationAssertion( "GO:0043038") +AnnotationAssertion(rdfs:label "amino acid activation") +SubClassOf( ) + +# Class: (tRNA aminoacylation) + +AnnotationAssertion( "GO:0043039") +AnnotationAssertion(rdfs:label "tRNA aminoacylation") +SubClassOf( ) +SubClassOf( ) + +# Class: (peptide biosynthetic process) + +AnnotationAssertion( "GO:0043043") +AnnotationAssertion(rdfs:label "peptide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of catalytic activity) + +AnnotationAssertion( "GO:0043085") +AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of catalytic activity) + +AnnotationAssertion( "GO:0043086") +AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (macromolecule metabolic process) + +AnnotationAssertion( "GO:0043170") +AnnotationAssertion(rdfs:label "macromolecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to amino acid) + +AnnotationAssertion( "GO:0043200") +AnnotationAssertion(rdfs:label "response to amino acid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to external biotic stimulus) + +AnnotationAssertion( "GO:0043207") +AnnotationAssertion(rdfs:label "response to external biotic stimulus") +SubClassOf( ) +SubClassOf( ) + +# Class: (organelle) + +AnnotationAssertion( "GO:0043226") +AnnotationAssertion(rdfs:label "organelle") +SubClassOf( ) +DisjointClasses( ) +DisjointUnion( ) + +# Class: (membrane-bounded organelle) + +AnnotationAssertion( "GO:0043227") +AnnotationAssertion(rdfs:label "membrane-bounded organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (membraneless organelle) + +AnnotationAssertion( "GO:0043228") +AnnotationAssertion(rdfs:label "membraneless organelle") +SubClassOf( ) + +# Class: (intracellular organelle) + +AnnotationAssertion( "GO:0043229") +AnnotationAssertion(rdfs:label "intracellular organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intracellular membrane-bounded organelle) + +AnnotationAssertion( "GO:0043231") +AnnotationAssertion(rdfs:label "intracellular membrane-bounded organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intracellular membraneless organelle) + +AnnotationAssertion( "GO:0043232") +AnnotationAssertion(rdfs:label "intracellular membraneless organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organelle lumen) + +AnnotationAssertion( "GO:0043233") +AnnotationAssertion(rdfs:label "organelle lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of protein-containing complex disassembly) + +AnnotationAssertion( "GO:0043242") +AnnotationAssertion(rdfs:label "negative regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein-containing complex disassembly) + +AnnotationAssertion( "GO:0043243") +AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein-containing complex disassembly) + +AnnotationAssertion( "GO:0043244") +AnnotationAssertion(rdfs:label "regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein-containing complex assembly) + +AnnotationAssertion( "GO:0043254") +AnnotationAssertion(rdfs:label "regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of carbohydrate biosynthetic process) + +AnnotationAssertion( "GO:0043255") +AnnotationAssertion(rdfs:label "regulation of carbohydrate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (oxoacid metabolic process) + +AnnotationAssertion( "GO:0043436") +AnnotationAssertion(rdfs:label "oxoacid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alkane biosynthetic process) + +AnnotationAssertion( "GO:0043447") +AnnotationAssertion(rdfs:label "alkane biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of secondary metabolic process) + +AnnotationAssertion( "GO:0043455") +AnnotationAssertion(rdfs:label "regulation of secondary metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cellular respiration) + +AnnotationAssertion( "GO:0043457") +AnnotationAssertion(rdfs:label "regulation of cellular respiration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of generation of precursor metabolites and energy) + +AnnotationAssertion( "GO:0043467") +AnnotationAssertion(rdfs:label "regulation of generation of precursor metabolites and energy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amide metabolic process) + +AnnotationAssertion( "GO:0043603") +AnnotationAssertion(rdfs:label "amide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amide biosynthetic process) + +AnnotationAssertion( "GO:0043604") +AnnotationAssertion(rdfs:label "amide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing complex organization) + +AnnotationAssertion( "GO:0043933") +AnnotationAssertion(rdfs:label "protein-containing complex organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component biogenesis) + +AnnotationAssertion( "GO:0044085") +AnnotationAssertion(rdfs:label "cellular component biogenesis") +SubClassOf( ) + +# Class: (regulation of cellular component biogenesis) + +AnnotationAssertion( "GO:0044087") +AnnotationAssertion(rdfs:label "regulation of cellular component biogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of vacuole organization) + +AnnotationAssertion( "GO:0044088") +AnnotationAssertion(rdfs:label "regulation of vacuole organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cellular component biogenesis) + +AnnotationAssertion( "GO:0044089") +AnnotationAssertion(rdfs:label "positive regulation of cellular component biogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of vacuole organization) + +AnnotationAssertion( "GO:0044090") +AnnotationAssertion(rdfs:label "positive regulation of vacuole organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane biogenesis) + +AnnotationAssertion( "GO:0044091") +AnnotationAssertion(rdfs:label "membrane biogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of molecular function) + +AnnotationAssertion( "GO:0044092") +AnnotationAssertion(rdfs:label "negative regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of molecular function) + +AnnotationAssertion( "GO:0044093") +AnnotationAssertion(rdfs:label "positive regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translation initiation ternary complex) + +AnnotationAssertion( "GO:0044207") +AnnotationAssertion(rdfs:label "translation initiation ternary complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (primary metabolic process) + +AnnotationAssertion( "GO:0044238") +AnnotationAssertion(rdfs:label "primary metabolic process") +SubClassOf( ) + +# Class: (sulfur compound biosynthetic process) + +AnnotationAssertion( "GO:0044272") +AnnotationAssertion(rdfs:label "sulfur compound biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (small molecule metabolic process) + +AnnotationAssertion( "GO:0044281") +AnnotationAssertion(rdfs:label "small molecule metabolic process") +SubClassOf( ) + +# Class: (small molecule biosynthetic process) + +AnnotationAssertion( "GO:0044283") +AnnotationAssertion(rdfs:label "small molecule biosynthetic process") +SubClassOf( ) +SubClassOf( ) + +# Class: (biological process involved in interspecies interaction between organisms) + +AnnotationAssertion( "GO:0044419") +AnnotationAssertion(rdfs:label "biological process involved in interspecies interaction between organisms") +SubClassOf( ) + +# Class: (virion component) + +AnnotationAssertion( "GO:0044423") +AnnotationAssertion(rdfs:label "virion component") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +DisjointClasses( ) + +# Class: (secondary metabolite biosynthetic process) + +AnnotationAssertion( "GO:0044550") +AnnotationAssertion(rdfs:label "secondary metabolite biosynthetic process") +SubClassOf( ) +SubClassOf( ) + +# Class: (leukocyte activation) + +AnnotationAssertion( "GO:0045321") +AnnotationAssertion(rdfs:label "leukocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular respiration) + +AnnotationAssertion( "GO:0045333") +AnnotationAssertion(rdfs:label "cellular respiration") +SubClassOf( ) + +# Class: (regulation of B cell differentiation) + +AnnotationAssertion( "GO:0045577") +AnnotationAssertion(rdfs:label "regulation of B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of B cell differentiation) + +AnnotationAssertion( "GO:0045578") +AnnotationAssertion(rdfs:label "negative regulation of B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of B cell differentiation) + +AnnotationAssertion( "GO:0045579") +AnnotationAssertion(rdfs:label "positive regulation of B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell differentiation) + +AnnotationAssertion( "GO:0045595") +AnnotationAssertion(rdfs:label "regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell differentiation) + +AnnotationAssertion( "GO:0045596") +AnnotationAssertion(rdfs:label "negative regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell differentiation) + +AnnotationAssertion( "GO:0045597") +AnnotationAssertion(rdfs:label "positive regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of lymphocyte differentiation) + +AnnotationAssertion( "GO:0045619") +AnnotationAssertion(rdfs:label "regulation of lymphocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lymphocyte differentiation) + +AnnotationAssertion( "GO:0045620") +AnnotationAssertion(rdfs:label "negative regulation of lymphocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lymphocyte differentiation) + +AnnotationAssertion( "GO:0045621") +AnnotationAssertion(rdfs:label "positive regulation of lymphocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translation) + +AnnotationAssertion( "GO:0045727") +AnnotationAssertion(rdfs:label "positive regulation of translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of amino acid metabolic process) + +AnnotationAssertion( "GO:0045763") +AnnotationAssertion(rdfs:label "negative regulation of amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of amino acid metabolic process) + +AnnotationAssertion( "GO:0045764") +AnnotationAssertion(rdfs:label "positive regulation of amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of angiogenesis) + +AnnotationAssertion( "GO:0045765") +AnnotationAssertion(rdfs:label "regulation of angiogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of angiogenesis) + +AnnotationAssertion( "GO:0045766") +AnnotationAssertion(rdfs:label "positive regulation of angiogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of gene expression, epigenetic) + +AnnotationAssertion( "GO:0045814") +AnnotationAssertion(rdfs:label "negative regulation of gene expression, epigenetic") +SubClassOf( ) +SubClassOf( ) + +# Class: (negative regulation of isoprenoid metabolic process) + +AnnotationAssertion( "GO:0045827") +AnnotationAssertion(rdfs:label "negative regulation of isoprenoid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lipid metabolic process) + +AnnotationAssertion( "GO:0045833") +AnnotationAssertion(rdfs:label "negative regulation of lipid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lipid metabolic process) + +AnnotationAssertion( "GO:0045834") +AnnotationAssertion(rdfs:label "positive regulation of lipid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of DNA-templated transcription) + +AnnotationAssertion( "GO:0045892") +AnnotationAssertion(rdfs:label "negative regulation of DNA-templated transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of DNA-templated transcription) + +AnnotationAssertion( "GO:0045893") +AnnotationAssertion(rdfs:label "positive regulation of DNA-templated transcription") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of translational elongation) + +AnnotationAssertion( "GO:0045900") +AnnotationAssertion(rdfs:label "negative regulation of translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational elongation) + +AnnotationAssertion( "GO:0045901") +AnnotationAssertion(rdfs:label "positive regulation of translational elongation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of translational termination) + +AnnotationAssertion( "GO:0045904") +AnnotationAssertion(rdfs:label "negative regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational termination) + +AnnotationAssertion( "GO:0045905") +AnnotationAssertion(rdfs:label "positive regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of DNA recombination) + +AnnotationAssertion( "GO:0045910") +AnnotationAssertion(rdfs:label "negative regulation of DNA recombination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of DNA recombination) + +AnnotationAssertion( "GO:0045911") +AnnotationAssertion(rdfs:label "positive regulation of DNA recombination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of carbohydrate metabolic process) + +AnnotationAssertion( "GO:0045912") +AnnotationAssertion(rdfs:label "negative regulation of carbohydrate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of carbohydrate metabolic process) + +AnnotationAssertion( "GO:0045913") +AnnotationAssertion(rdfs:label "positive regulation of carbohydrate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of nucleobase-containing compound metabolic process) + +AnnotationAssertion( "GO:0045934") +AnnotationAssertion(rdfs:label "negative regulation of nucleobase-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of phosphate metabolic process) + +AnnotationAssertion( "GO:0045936") +AnnotationAssertion(rdfs:label "negative regulation of phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of phosphate metabolic process) + +AnnotationAssertion( "GO:0045937") +AnnotationAssertion(rdfs:label "positive regulation of phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of translational initiation) + +AnnotationAssertion( "GO:0045947") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational initiation) + +AnnotationAssertion( "GO:0045948") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of nucleoside metabolic process) + +AnnotationAssertion( "GO:0045978") +AnnotationAssertion(rdfs:label "negative regulation of nucleoside metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of nucleoside metabolic process) + +AnnotationAssertion( "GO:0045979") +AnnotationAssertion(rdfs:label "positive regulation of nucleoside metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of nucleotide metabolic process) + +AnnotationAssertion( "GO:0045980") +AnnotationAssertion(rdfs:label "negative regulation of nucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of nucleotide metabolic process) + +AnnotationAssertion( "GO:0045981") +AnnotationAssertion(rdfs:label "positive regulation of nucleotide metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase biosynthetic process) + +AnnotationAssertion( "GO:0046112") +AnnotationAssertion(rdfs:label "nucleobase biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of vitamin metabolic process) + +AnnotationAssertion( "GO:0046136") +AnnotationAssertion(rdfs:label "positive regulation of vitamin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of vitamin metabolic process) + +AnnotationAssertion( "GO:0046137") +AnnotationAssertion(rdfs:label "negative regulation of vitamin metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyanide biosynthetic process) + +AnnotationAssertion( "GO:0046202") +AnnotationAssertion(rdfs:label "cyanide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pyridine biosynthetic process) + +AnnotationAssertion( "GO:0046220") +AnnotationAssertion(rdfs:label "pyridine biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monosaccharide biosynthetic process) + +AnnotationAssertion( "GO:0046364") +AnnotationAssertion(rdfs:label "monosaccharide biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (deoxyribose phosphate biosynthetic process) + +AnnotationAssertion( "GO:0046385") +AnnotationAssertion(rdfs:label "deoxyribose phosphate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carboxylic acid biosynthetic process) + +AnnotationAssertion( "GO:0046394") +AnnotationAssertion(rdfs:label "carboxylic acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (creatinine metabolic process) + +AnnotationAssertion( "GO:0046449") +AnnotationAssertion(rdfs:label "creatinine metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte activation) + +AnnotationAssertion( "GO:0046649") +AnnotationAssertion(rdfs:label "lymphocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to carbamate) + +AnnotationAssertion( "GO:0046681") +AnnotationAssertion(rdfs:label "response to carbamate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to organophosphorus) + +AnnotationAssertion( "GO:0046683") +AnnotationAssertion(rdfs:label "response to organophosphorus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lipid biosynthetic process) + +AnnotationAssertion( "GO:0046889") +AnnotationAssertion(rdfs:label "positive regulation of lipid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of lipid biosynthetic process) + +AnnotationAssertion( "GO:0046890") +AnnotationAssertion(rdfs:label "regulation of lipid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (somatic stem cell division) + +AnnotationAssertion( "GO:0048103") +AnnotationAssertion(rdfs:label "somatic stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell development) + +AnnotationAssertion( "GO:0048468") +AnnotationAssertion(rdfs:label "cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (blood vessel morphogenesis) + +AnnotationAssertion( "GO:0048514") +AnnotationAssertion(rdfs:label "blood vessel morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of biological process) + +AnnotationAssertion( "GO:0048518") +AnnotationAssertion(rdfs:label "positive regulation of biological process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of biological process) + +AnnotationAssertion( "GO:0048519") +AnnotationAssertion(rdfs:label "negative regulation of biological process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cellular process) + +AnnotationAssertion( "GO:0048522") +AnnotationAssertion(rdfs:label "positive regulation of cellular process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cellular process) + +AnnotationAssertion( "GO:0048523") +AnnotationAssertion(rdfs:label "negative regulation of cellular process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to stimulus) + +AnnotationAssertion( "GO:0048583") +AnnotationAssertion(rdfs:label "regulation of response to stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to stimulus) + +AnnotationAssertion( "GO:0048584") +AnnotationAssertion(rdfs:label "positive regulation of response to stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to stimulus) + +AnnotationAssertion( "GO:0048585") +AnnotationAssertion(rdfs:label "negative regulation of response to stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure formation involved in morphogenesis) + +AnnotationAssertion( "GO:0048646") +AnnotationAssertion(rdfs:label "anatomical structure formation involved in morphogenesis") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tissue morphogenesis) + +AnnotationAssertion( "GO:0048729") +AnnotationAssertion(rdfs:label "tissue morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (system development) + +AnnotationAssertion( "GO:0048731") +AnnotationAssertion(rdfs:label "system development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure development) + +AnnotationAssertion( "GO:0048856") +AnnotationAssertion(rdfs:label "anatomical structure development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (stem cell differentiation) + +AnnotationAssertion( "GO:0048863") +AnnotationAssertion(rdfs:label "stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (stem cell development) + +AnnotationAssertion( "GO:0048864") +AnnotationAssertion(rdfs:label "stem cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular developmental process) + +AnnotationAssertion( "GO:0048869") +AnnotationAssertion(rdfs:label "cellular developmental process") +SubClassOf( ) +SubClassOf( ) + +# Class: (cell motility) + +AnnotationAssertion( "GO:0048870") +AnnotationAssertion(rdfs:label "cell motility") +SubClassOf( ) + +# Class: (regulation of immune response) + +AnnotationAssertion( "GO:0050776") +AnnotationAssertion(rdfs:label "regulation of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of immune response) + +AnnotationAssertion( "GO:0050777") +AnnotationAssertion(rdfs:label "negative regulation of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of immune response) + +AnnotationAssertion( "GO:0050778") +AnnotationAssertion(rdfs:label "positive regulation of immune response") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of biological process) + +AnnotationAssertion( "GO:0050789") +AnnotationAssertion(rdfs:label "regulation of biological process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of catalytic activity) + +AnnotationAssertion( "GO:0050790") +AnnotationAssertion(rdfs:label "regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of developmental process) + +AnnotationAssertion( "GO:0050793") +AnnotationAssertion(rdfs:label "regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cellular process) + +AnnotationAssertion( "GO:0050794") +AnnotationAssertion(rdfs:label "regulation of cellular process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of B cell activation) + +AnnotationAssertion( "GO:0050864") +AnnotationAssertion(rdfs:label "regulation of B cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell activation) + +AnnotationAssertion( "GO:0050865") +AnnotationAssertion(rdfs:label "regulation of cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell activation) + +AnnotationAssertion( "GO:0050866") +AnnotationAssertion(rdfs:label "negative regulation of cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell activation) + +AnnotationAssertion( "GO:0050867") +AnnotationAssertion(rdfs:label "positive regulation of cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of B cell activation) + +AnnotationAssertion( "GO:0050869") +AnnotationAssertion(rdfs:label "negative regulation of B cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of B cell activation) + +AnnotationAssertion( "GO:0050871") +AnnotationAssertion(rdfs:label "positive regulation of B cell activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to stimulus) + +AnnotationAssertion( "GO:0050896") +AnnotationAssertion(rdfs:label "response to stimulus") +SubClassOf( ) + +# Class: (nitrile metabolic process) + +AnnotationAssertion( "GO:0050898") +AnnotationAssertion(rdfs:label "nitrile metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of DNA metabolic process) + +AnnotationAssertion( "GO:0051052") +AnnotationAssertion(rdfs:label "regulation of DNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of DNA metabolic process) + +AnnotationAssertion( "GO:0051053") +AnnotationAssertion(rdfs:label "negative regulation of DNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of DNA metabolic process) + +AnnotationAssertion( "GO:0051054") +AnnotationAssertion(rdfs:label "positive regulation of DNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lipid biosynthetic process) + +AnnotationAssertion( "GO:0051055") +AnnotationAssertion(rdfs:label "negative regulation of lipid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear membrane disassembly) + +AnnotationAssertion( "GO:0051081") +AnnotationAssertion(rdfs:label "nuclear membrane disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of developmental process) + +AnnotationAssertion( "GO:0051093") +AnnotationAssertion(rdfs:label "negative regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of developmental process) + +AnnotationAssertion( "GO:0051094") +AnnotationAssertion(rdfs:label "positive regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cellular component organization) + +AnnotationAssertion( "GO:0051128") +AnnotationAssertion(rdfs:label "regulation of cellular component organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cellular component organization) + +AnnotationAssertion( "GO:0051129") +AnnotationAssertion(rdfs:label "negative regulation of cellular component organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cellular component organization) + +AnnotationAssertion( "GO:0051130") +AnnotationAssertion(rdfs:label "positive regulation of cellular component organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of phosphorus metabolic process) + +AnnotationAssertion( "GO:0051174") +AnnotationAssertion(rdfs:label "regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of multicellular organismal process) + +AnnotationAssertion( "GO:0051239") +AnnotationAssertion(rdfs:label "regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of multicellular organismal process) + +AnnotationAssertion( "GO:0051240") +AnnotationAssertion(rdfs:label "positive regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of multicellular organismal process) + +AnnotationAssertion( "GO:0051241") +AnnotationAssertion(rdfs:label "negative regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein metabolic process) + +AnnotationAssertion( "GO:0051246") +AnnotationAssertion(rdfs:label "regulation of protein metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein metabolic process) + +AnnotationAssertion( "GO:0051247") +AnnotationAssertion(rdfs:label "positive regulation of protein metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of protein metabolic process) + +AnnotationAssertion( "GO:0051248") +AnnotationAssertion(rdfs:label "negative regulation of protein metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of lymphocyte activation) + +AnnotationAssertion( "GO:0051249") +AnnotationAssertion(rdfs:label "regulation of lymphocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lymphocyte activation) + +AnnotationAssertion( "GO:0051250") +AnnotationAssertion(rdfs:label "negative regulation of lymphocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lymphocyte activation) + +AnnotationAssertion( "GO:0051251") +AnnotationAssertion(rdfs:label "positive regulation of lymphocyte activation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of RNA metabolic process) + +AnnotationAssertion( "GO:0051252") +AnnotationAssertion(rdfs:label "regulation of RNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of RNA metabolic process) + +AnnotationAssertion( "GO:0051253") +AnnotationAssertion(rdfs:label "negative regulation of RNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of RNA metabolic process) + +AnnotationAssertion( "GO:0051254") +AnnotationAssertion(rdfs:label "positive regulation of RNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromosome organization) + +AnnotationAssertion( "GO:0051276") +AnnotationAssertion(rdfs:label "chromosome organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell division) + +AnnotationAssertion( "GO:0051301") +AnnotationAssertion(rdfs:label "cell division") +SubClassOf( ) + +# Class: (regulation of cell division) + +AnnotationAssertion( "GO:0051302") +AnnotationAssertion(rdfs:label "regulation of cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of transferase activity) + +AnnotationAssertion( "GO:0051338") +AnnotationAssertion(rdfs:label "regulation of transferase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to other organism) + +AnnotationAssertion( "GO:0051707") +AnnotationAssertion(rdfs:label "response to other organism") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to stimulus) + +AnnotationAssertion( "GO:0051716") +AnnotationAssertion(rdfs:label "cellular response to stimulus") +SubClassOf( ) +SubClassOf( ) + +# Class: (positive regulation of cell division) + +AnnotationAssertion( "GO:0051781") +AnnotationAssertion(rdfs:label "positive regulation of cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell division) + +AnnotationAssertion( "GO:0051782") +AnnotationAssertion(rdfs:label "negative regulation of cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase-containing small molecule metabolic process) + +AnnotationAssertion( "GO:0055086") +AnnotationAssertion(rdfs:label "nucleobase-containing small molecule metabolic process") +SubClassOf( ) +SubClassOf( ) + +# Class: (hematopoietic stem cell differentiation) + +AnnotationAssertion( "GO:0060218") +AnnotationAssertion(rdfs:label "hematopoietic stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of macromolecule metabolic process) + +AnnotationAssertion( "GO:0060255") +AnnotationAssertion(rdfs:label "regulation of macromolecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell development) + +AnnotationAssertion( "GO:0060284") +AnnotationAssertion(rdfs:label "regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to ammonium ion) + +AnnotationAssertion( "GO:0060359") +AnnotationAssertion(rdfs:label "response to ammonium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane organization) + +AnnotationAssertion( "GO:0061024") +AnnotationAssertion(rdfs:label "membrane organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (connective tissue development) + +AnnotationAssertion( "GO:0061448") +AnnotationAssertion(rdfs:label "connective tissue development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (transferase complex, transferring phosphorus-containing groups) + +AnnotationAssertion( "GO:0061695") +AnnotationAssertion(rdfs:label "transferase complex, transferring phosphorus-containing groups") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of small molecule metabolic process) + +AnnotationAssertion( "GO:0062012") +AnnotationAssertion(rdfs:label "regulation of small molecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of small molecule metabolic process) + +AnnotationAssertion( "GO:0062013") +AnnotationAssertion(rdfs:label "positive regulation of small molecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of small molecule metabolic process) + +AnnotationAssertion( "GO:0062014") +AnnotationAssertion(rdfs:label "negative regulation of small molecule metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing complex assembly) + +AnnotationAssertion( "GO:0065003") +AnnotationAssertion(rdfs:label "protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biological regulation) + +AnnotationAssertion( "GO:0065007") +AnnotationAssertion(rdfs:label "biological regulation") +SubClassOf( ) + +# Class: (regulation of molecular function) + +AnnotationAssertion( "GO:0065009") +AnnotationAssertion(rdfs:label "regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intracellular organelle lumen) + +AnnotationAssertion( "GO:0070013") +AnnotationAssertion(rdfs:label "intracellular organelle lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (halogen metabolic process) + +AnnotationAssertion( "GO:0070276") +AnnotationAssertion(rdfs:label "halogen metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to biotin) + +AnnotationAssertion( "GO:0070781") +AnnotationAssertion(rdfs:label "response to biotin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (heterochromatin organization) + +AnnotationAssertion( "GO:0070828") +AnnotationAssertion(rdfs:label "heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to chemical stimulus) + +AnnotationAssertion( "GO:0070887") +AnnotationAssertion(rdfs:label "cellular response to chemical stimulus") +SubClassOf( ) +SubClassOf( ) + +# Class: (organelle assembly) + +AnnotationAssertion( "GO:0070925") +AnnotationAssertion(rdfs:label "organelle assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to abiotic stimulus) + +AnnotationAssertion( "GO:0071214") +AnnotationAssertion(rdfs:label "cellular response to abiotic stimulus") +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to acid chemical) + +AnnotationAssertion( "GO:0071229") +AnnotationAssertion(rdfs:label "cellular response to acid chemical") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to amino acid stimulus) + +AnnotationAssertion( "GO:0071230") +AnnotationAssertion(rdfs:label "cellular response to amino acid stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to ammonium ion) + +AnnotationAssertion( "GO:0071242") +AnnotationAssertion(rdfs:label "cellular response to ammonium ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to metal ion) + +AnnotationAssertion( "GO:0071248") +AnnotationAssertion(rdfs:label "cellular response to metal ion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to nitrate) + +AnnotationAssertion( "GO:0071249") +AnnotationAssertion(rdfs:label "cellular response to nitrate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to vitamin) + +AnnotationAssertion( "GO:0071295") +AnnotationAssertion(rdfs:label "cellular response to vitamin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to biotin) + +AnnotationAssertion( "GO:0071296") +AnnotationAssertion(rdfs:label "cellular response to biotin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to acetate) + +AnnotationAssertion( "GO:0071311") +AnnotationAssertion(rdfs:label "cellular response to acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to carbohydrate stimulus) + +AnnotationAssertion( "GO:0071322") +AnnotationAssertion(rdfs:label "cellular response to carbohydrate stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to monosaccharide stimulus) + +AnnotationAssertion( "GO:0071326") +AnnotationAssertion(rdfs:label "cellular response to monosaccharide stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (diphosphate metabolic process) + +AnnotationAssertion( "GO:0071344") +AnnotationAssertion(rdfs:label "diphosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to lipid) + +AnnotationAssertion( "GO:0071396") +AnnotationAssertion(rdfs:label "cellular response to lipid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to amine stimulus) + +AnnotationAssertion( "GO:0071418") +AnnotationAssertion(rdfs:label "cellular response to amine stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to water stimulus) + +AnnotationAssertion( "GO:0071462") +AnnotationAssertion(rdfs:label "cellular response to water stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular response to xenobiotic stimulus) + +AnnotationAssertion( "GO:0071466") +AnnotationAssertion(rdfs:label "cellular response to xenobiotic stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (membrane assembly) + +AnnotationAssertion( "GO:0071709") +AnnotationAssertion(rdfs:label "membrane assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear membrane organization) + +AnnotationAssertion( "GO:0071763") +AnnotationAssertion(rdfs:label "nuclear membrane organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-RNA complex organization) + +AnnotationAssertion( "GO:0071826") +AnnotationAssertion(rdfs:label "protein-RNA complex organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component organization or biogenesis) + +AnnotationAssertion( "GO:0071840") +AnnotationAssertion(rdfs:label "cellular component organization or biogenesis") +SubClassOf( ) + +# Class: (DNA biosynthetic process) + +AnnotationAssertion( "GO:0071897") +AnnotationAssertion(rdfs:label "DNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrogen cycle metabolic process) + +AnnotationAssertion( "GO:0071941") +AnnotationAssertion(rdfs:label "nitrogen cycle metabolic process") +SubClassOf( ) + +# Class: (cell periphery) + +AnnotationAssertion( "GO:0071944") +AnnotationAssertion(rdfs:label "cell periphery") +SubClassOf( ) + +# Class: (monocarboxylic acid biosynthetic process) + +AnnotationAssertion( "GO:0072330") +AnnotationAssertion(rdfs:label "monocarboxylic acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lactam metabolic process) + +AnnotationAssertion( "GO:0072338") +AnnotationAssertion(rdfs:label "lactam metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lactam biosynthetic process) + +AnnotationAssertion( "GO:0072339") +AnnotationAssertion(rdfs:label "lactam biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (circulatory system development) + +AnnotationAssertion( "GO:0072359") +AnnotationAssertion(rdfs:label "circulatory system development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pyridine-containing compound metabolic process) + +AnnotationAssertion( "GO:0072524") +AnnotationAssertion(rdfs:label "pyridine-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pyridine-containing compound biosynthetic process) + +AnnotationAssertion( "GO:0072525") +AnnotationAssertion(rdfs:label "pyridine-containing compound biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nitrile biosynthetic process) + +AnnotationAssertion( "GO:0080028") +AnnotationAssertion(rdfs:label "nitrile biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of primary metabolic process) + +AnnotationAssertion( "GO:0080090") +AnnotationAssertion(rdfs:label "regulation of primary metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleic acid metabolic process) + +AnnotationAssertion( "GO:0090304") +AnnotationAssertion(rdfs:label "nucleic acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organohalogen metabolic process) + +AnnotationAssertion( "GO:0090345") +AnnotationAssertion(rdfs:label "organohalogen metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of organohalogen metabolic process) + +AnnotationAssertion( "GO:0090347") +AnnotationAssertion(rdfs:label "regulation of organohalogen metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organophosphate biosynthetic process) + +AnnotationAssertion( "GO:0090407") +AnnotationAssertion(rdfs:label "organophosphate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to toxic substance) + +AnnotationAssertion( "GO:0097237") +AnnotationAssertion(rdfs:label "cellular response to toxic substance") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (plasma membrane region) + +AnnotationAssertion( "GO:0098590") +AnnotationAssertion(rdfs:label "plasma membrane region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane protein complex) + +AnnotationAssertion( "GO:0098796") +AnnotationAssertion(rdfs:label "membrane protein complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plasma membrane protein complex) + +AnnotationAssertion( "GO:0098797") +AnnotationAssertion(rdfs:label "plasma membrane protein complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial protein-containing complex) + +AnnotationAssertion( "GO:0098798") +AnnotationAssertion(rdfs:label "mitochondrial protein-containing complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cytoplasmic region) + +AnnotationAssertion( "GO:0099568") +AnnotationAssertion(rdfs:label "cytoplasmic region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell cortex region) + +AnnotationAssertion( "GO:0099738") +AnnotationAssertion(rdfs:label "cell cortex region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear membrane biogenesis) + +AnnotationAssertion( "GO:0101025") +AnnotationAssertion(rdfs:label "nuclear membrane biogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to environmental stimulus) + +AnnotationAssertion( "GO:0104004") +AnnotationAssertion(rdfs:label "cellular response to environmental stimulus") +SubClassOf( ) + +# Class: (cellular anatomical structure) + +AnnotationAssertion( "GO:0110165") +AnnotationAssertion(rdfs:label "cellular anatomical structure") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (hydrocarbon biosynthetic process) + +AnnotationAssertion( "GO:0120251") +AnnotationAssertion(rdfs:label "hydrocarbon biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hydrocarbon metabolic process) + +AnnotationAssertion( "GO:0120252") +AnnotationAssertion(rdfs:label "hydrocarbon metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of heterochromatin organization) + +AnnotationAssertion( "GO:0120261") +AnnotationAssertion(rdfs:label "regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of heterochromatin organization) + +AnnotationAssertion( "GO:0120262") +AnnotationAssertion(rdfs:label "negative regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of heterochromatin organization) + +AnnotationAssertion( "GO:0120263") +AnnotationAssertion(rdfs:label "positive regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on a protein) + +AnnotationAssertion( "GO:0140096") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on DNA) + +AnnotationAssertion( "GO:0140097") +AnnotationAssertion(rdfs:label "catalytic activity, acting on DNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on RNA) + +AnnotationAssertion( "GO:0140098") +AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on a tRNA) + +AnnotationAssertion( "GO:0140101") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a tRNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear protein-containing complex) + +AnnotationAssertion( "GO:0140513") +AnnotationAssertion(rdfs:label "nuclear protein-containing complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on a nucleic acid) + +AnnotationAssertion( "GO:0140640") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a nucleic acid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membraneless organelle assembly) + +AnnotationAssertion( "GO:0140694") +AnnotationAssertion(rdfs:label "membraneless organelle assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleic acid biosynthetic process) + +AnnotationAssertion( "GO:0141187") +AnnotationAssertion(rdfs:label "nucleic acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein biosynthetic process) + +AnnotationAssertion( "GO:0160307") +AnnotationAssertion(rdfs:label "protein biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (proteinogenic amino acid biosynthetic process) + +AnnotationAssertion( "GO:0170038") +AnnotationAssertion(rdfs:label "proteinogenic amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (proteinogenic amino acid metabolic process) + +AnnotationAssertion( "GO:0170039") +AnnotationAssertion(rdfs:label "proteinogenic amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of secondary metabolite biosynthetic process) + +AnnotationAssertion( "GO:1900376") +AnnotationAssertion(rdfs:label "regulation of secondary metabolite biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of secondary metabolite biosynthetic process) + +AnnotationAssertion( "GO:1900377") +AnnotationAssertion(rdfs:label "negative regulation of secondary metabolite biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of secondary metabolite biosynthetic process) + +AnnotationAssertion( "GO:1900378") +AnnotationAssertion(rdfs:label "positive regulation of secondary metabolite biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate derivative metabolic process) + +AnnotationAssertion( "GO:1901135") +AnnotationAssertion(rdfs:label "carbohydrate derivative metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (carbohydrate derivative biosynthetic process) + +AnnotationAssertion( "GO:1901137") +AnnotationAssertion(rdfs:label "carbohydrate derivative biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of formation of translation initiation ternary complex) + +AnnotationAssertion( "GO:1901190") +AnnotationAssertion(rdfs:label "regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of formation of translation initiation ternary complex) + +AnnotationAssertion( "GO:1901191") +AnnotationAssertion(rdfs:label "negative regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of formation of translation initiation ternary complex) + +AnnotationAssertion( "GO:1901192") +AnnotationAssertion(rdfs:label "positive regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoside phosphate biosynthetic process) + +AnnotationAssertion( "GO:1901293") +AnnotationAssertion(rdfs:label "nucleoside phosphate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of vasculature development) + +AnnotationAssertion( "GO:1901342") +AnnotationAssertion(rdfs:label "regulation of vasculature development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of vasculature development) + +AnnotationAssertion( "GO:1901343") +AnnotationAssertion(rdfs:label "negative regulation of vasculature development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to acetate) + +AnnotationAssertion( "GO:1901457") +AnnotationAssertion(rdfs:label "regulation of response to acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to acetate) + +AnnotationAssertion( "GO:1901458") +AnnotationAssertion(rdfs:label "negative regulation of response to acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to acetate) + +AnnotationAssertion( "GO:1901459") +AnnotationAssertion(rdfs:label "positive regulation of response to acetate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of hematopoietic progenitor cell differentiation) + +AnnotationAssertion( "GO:1901532") +AnnotationAssertion(rdfs:label "regulation of hematopoietic progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of hematopoietic progenitor cell differentiation) + +AnnotationAssertion( "GO:1901533") +AnnotationAssertion(rdfs:label "negative regulation of hematopoietic progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of hematopoietic progenitor cell differentiation) + +AnnotationAssertion( "GO:1901534") +AnnotationAssertion(rdfs:label "positive regulation of hematopoietic progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of alkane biosynthetic process) + +AnnotationAssertion( "GO:1901577") +AnnotationAssertion(rdfs:label "regulation of alkane biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of alkane biosynthetic process) + +AnnotationAssertion( "GO:1901578") +AnnotationAssertion(rdfs:label "negative regulation of alkane biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of alkane biosynthetic process) + +AnnotationAssertion( "GO:1901579") +AnnotationAssertion(rdfs:label "positive regulation of alkane biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino acid metabolic process) + +AnnotationAssertion( "GO:1901605") +AnnotationAssertion(rdfs:label "alpha-amino acid metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (alpha-amino acid biosynthetic process) + +AnnotationAssertion( "GO:1901607") +AnnotationAssertion(rdfs:label "alpha-amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to peptide) + +AnnotationAssertion( "GO:1901652") +AnnotationAssertion(rdfs:label "response to peptide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to peptide) + +AnnotationAssertion( "GO:1901653") +AnnotationAssertion(rdfs:label "cellular response to peptide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (glycosyl compound biosynthetic process) + +AnnotationAssertion( "GO:1901659") +AnnotationAssertion(rdfs:label "glycosyl compound biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to nitrogen compound) + +AnnotationAssertion( "GO:1901698") +AnnotationAssertion(rdfs:label "response to nitrogen compound") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to nitrogen compound) + +AnnotationAssertion( "GO:1901699") +AnnotationAssertion(rdfs:label "cellular response to nitrogen compound") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (response to oxygen-containing compound) + +AnnotationAssertion( "GO:1901700") +AnnotationAssertion(rdfs:label "response to oxygen-containing compound") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to oxygen-containing compound) + +AnnotationAssertion( "GO:1901701") +AnnotationAssertion(rdfs:label "cellular response to oxygen-containing compound") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (negative regulation of cellular respiration) + +AnnotationAssertion( "GO:1901856") +AnnotationAssertion(rdfs:label "negative regulation of cellular respiration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cellular respiration) + +AnnotationAssertion( "GO:1901857") +AnnotationAssertion(rdfs:label "positive regulation of cellular respiration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of hematopoietic stem cell differentiation) + +AnnotationAssertion( "GO:1902036") +AnnotationAssertion(rdfs:label "regulation of hematopoietic stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of hematopoietic stem cell differentiation) + +AnnotationAssertion( "GO:1902037") +AnnotationAssertion(rdfs:label "negative regulation of hematopoietic stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of hematopoietic stem cell differentiation) + +AnnotationAssertion( "GO:1902038") +AnnotationAssertion(rdfs:label "positive regulation of hematopoietic stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to salt) + +AnnotationAssertion( "GO:1902074") +AnnotationAssertion(rdfs:label "response to salt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to salt) + +AnnotationAssertion( "GO:1902075") +AnnotationAssertion(rdfs:label "cellular response to salt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (regulation of leukocyte differentiation) + +AnnotationAssertion( "GO:1902105") +AnnotationAssertion(rdfs:label "regulation of leukocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of leukocyte differentiation) + +AnnotationAssertion( "GO:1902106") +AnnotationAssertion(rdfs:label "negative regulation of leukocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of leukocyte differentiation) + +AnnotationAssertion( "GO:1902107") +AnnotationAssertion(rdfs:label "positive regulation of leukocyte differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of organelle assembly) + +AnnotationAssertion( "GO:1902115") +AnnotationAssertion(rdfs:label "regulation of organelle assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of organelle assembly) + +AnnotationAssertion( "GO:1902116") +AnnotationAssertion(rdfs:label "negative regulation of organelle assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of organelle assembly) + +AnnotationAssertion( "GO:1902117") +AnnotationAssertion(rdfs:label "positive regulation of organelle assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to reactive nitrogen species) + +AnnotationAssertion( "GO:1902170") +AnnotationAssertion(rdfs:label "cellular response to reactive nitrogen species") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of chromatin organization) + +AnnotationAssertion( "GO:1902275") +AnnotationAssertion(rdfs:label "regulation of chromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic complex) + +AnnotationAssertion( "GO:1902494") +AnnotationAssertion(rdfs:label "catalytic complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of RNA biosynthetic process) + +AnnotationAssertion( "GO:1902679") +AnnotationAssertion(rdfs:label "negative regulation of RNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of RNA biosynthetic process) + +AnnotationAssertion( "GO:1902680") +AnnotationAssertion(rdfs:label "positive regulation of RNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to alkane) + +AnnotationAssertion( "GO:1902778") +AnnotationAssertion(rdfs:label "response to alkane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to alkane) + +AnnotationAssertion( "GO:1902779") +AnnotationAssertion(rdfs:label "cellular response to alkane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (organelle disassembly) + +AnnotationAssertion( "GO:1903008") +AnnotationAssertion(rdfs:label "organelle disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mononuclear cell differentiation) + +AnnotationAssertion( "GO:1903131") +AnnotationAssertion(rdfs:label "mononuclear cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nitrogen cycle metabolic process) + +AnnotationAssertion( "GO:1903314") +AnnotationAssertion(rdfs:label "regulation of nitrogen cycle metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of nitrogen cycle metabolic process) + +AnnotationAssertion( "GO:1903315") +AnnotationAssertion(rdfs:label "negative regulation of nitrogen cycle metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of nitrogen cycle metabolic process) + +AnnotationAssertion( "GO:1903316") +AnnotationAssertion(rdfs:label "positive regulation of nitrogen cycle metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of tRNA metabolic process) + +AnnotationAssertion( "GO:1903326") +AnnotationAssertion(rdfs:label "regulation of tRNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of tRNA metabolic process) + +AnnotationAssertion( "GO:1903327") +AnnotationAssertion(rdfs:label "negative regulation of tRNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of tRNA metabolic process) + +AnnotationAssertion( "GO:1903328") +AnnotationAssertion(rdfs:label "positive regulation of tRNA metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of nucleus organization) + +AnnotationAssertion( "GO:1903353") +AnnotationAssertion(rdfs:label "regulation of nucleus organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of hemopoiesis) + +AnnotationAssertion( "GO:1903706") +AnnotationAssertion(rdfs:label "regulation of hemopoiesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of hemopoiesis) + +AnnotationAssertion( "GO:1903707") +AnnotationAssertion(rdfs:label "negative regulation of hemopoiesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of hemopoiesis) + +AnnotationAssertion( "GO:1903708") +AnnotationAssertion(rdfs:label "positive regulation of hemopoiesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of plasma membrane organization) + +AnnotationAssertion( "GO:1903729") +AnnotationAssertion(rdfs:label "regulation of plasma membrane organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to cyanide) + +AnnotationAssertion( "GO:1903927") +AnnotationAssertion(rdfs:label "response to cyanide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to cyanide) + +AnnotationAssertion( "GO:1903928") +AnnotationAssertion(rdfs:label "cellular response to cyanide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (positive regulation of vasculature development) + +AnnotationAssertion( "GO:1904018") +AnnotationAssertion(rdfs:label "positive regulation of vasculature development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of somatic stem cell division) + +AnnotationAssertion( "GO:1904675") +AnnotationAssertion(rdfs:label "regulation of somatic stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of somatic stem cell division) + +AnnotationAssertion( "GO:1904676") +AnnotationAssertion(rdfs:label "negative regulation of somatic stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of somatic stem cell division) + +AnnotationAssertion( "GO:1904677") +AnnotationAssertion(rdfs:label "positive regulation of somatic stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast disassembly) + +AnnotationAssertion( "GO:1904821") +AnnotationAssertion(rdfs:label "chloroplast disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of chromatin organization) + +AnnotationAssertion( "GO:1905268") +AnnotationAssertion(rdfs:label "negative regulation of chromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of chromatin organization) + +AnnotationAssertion( "GO:1905269") +AnnotationAssertion(rdfs:label "positive regulation of chromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to glycine) + +AnnotationAssertion( "GO:1905429") +AnnotationAssertion(rdfs:label "response to glycine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to glycine) + +AnnotationAssertion( "GO:1905430") +AnnotationAssertion(rdfs:label "cellular response to glycine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (regulation of lymphoid progenitor cell differentiation) + +AnnotationAssertion( "GO:1905456") +AnnotationAssertion(rdfs:label "regulation of lymphoid progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of lymphoid progenitor cell differentiation) + +AnnotationAssertion( "GO:1905457") +AnnotationAssertion(rdfs:label "negative regulation of lymphoid progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of lymphoid progenitor cell differentiation) + +AnnotationAssertion( "GO:1905458") +AnnotationAssertion(rdfs:label "positive regulation of lymphoid progenitor cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleus disassembly) + +AnnotationAssertion( "GO:1905690") +AnnotationAssertion(rdfs:label "nucleus disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (transferase complex) + +AnnotationAssertion( "GO:1990234") +AnnotationAssertion(rdfs:label "transferase complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (response to dsDNA) + +AnnotationAssertion( "GO:1990784") +AnnotationAssertion(rdfs:label "response to dsDNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular response to dsDNA) + +AnnotationAssertion( "GO:1990786") +AnnotationAssertion(rdfs:label "cellular response to dsDNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (ribonucleoprotein complex) + +AnnotationAssertion( "GO:1990904") +AnnotationAssertion(rdfs:label "ribonucleoprotein complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of multicellular organismal development) + +AnnotationAssertion( "GO:2000026") +AnnotationAssertion(rdfs:label "regulation of multicellular organismal development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of stem cell division) + +AnnotationAssertion( "GO:2000035") +AnnotationAssertion(rdfs:label "regulation of stem cell division") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cell motility) + +AnnotationAssertion( "GO:2000145") +AnnotationAssertion(rdfs:label "regulation of cell motility") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell motility) + +AnnotationAssertion( "GO:2000146") +AnnotationAssertion(rdfs:label "negative regulation of cell motility") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell motility) + +AnnotationAssertion( "GO:2000147") +AnnotationAssertion(rdfs:label "positive regulation of cell motility") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of blood vessel morphogenesis) + +AnnotationAssertion( "GO:2000181") +AnnotationAssertion(rdfs:label "negative regulation of blood vessel morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of reproductive process) + +AnnotationAssertion( "GO:2000241") +AnnotationAssertion(rdfs:label "regulation of reproductive process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of reproductive process) + +AnnotationAssertion( "GO:2000242") +AnnotationAssertion(rdfs:label "negative regulation of reproductive process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of reproductive process) + +AnnotationAssertion( "GO:2000243") +AnnotationAssertion(rdfs:label "positive regulation of reproductive process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of DNA biosynthetic process) + +AnnotationAssertion( "GO:2000278") +AnnotationAssertion(rdfs:label "regulation of DNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of DNA biosynthetic process) + +AnnotationAssertion( "GO:2000279") +AnnotationAssertion(rdfs:label "negative regulation of DNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of amino acid biosynthetic process) + +AnnotationAssertion( "GO:2000282") +AnnotationAssertion(rdfs:label "regulation of amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of amino acid biosynthetic process) + +AnnotationAssertion( "GO:2000283") +AnnotationAssertion(rdfs:label "negative regulation of amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of amino acid biosynthetic process) + +AnnotationAssertion( "GO:2000284") +AnnotationAssertion(rdfs:label "positive regulation of amino acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of DNA biosynthetic process) + +AnnotationAssertion( "GO:2000573") +AnnotationAssertion(rdfs:label "positive regulation of DNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of stem cell differentiation) + +AnnotationAssertion( "GO:2000736") +AnnotationAssertion(rdfs:label "regulation of stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of stem cell differentiation) + +AnnotationAssertion( "GO:2000737") +AnnotationAssertion(rdfs:label "negative regulation of stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of stem cell differentiation) + +AnnotationAssertion( "GO:2000738") +AnnotationAssertion(rdfs:label "positive regulation of stem cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of pro-B cell differentiation) + +AnnotationAssertion( "GO:2000973") +AnnotationAssertion(rdfs:label "regulation of pro-B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of pro-B cell differentiation) + +AnnotationAssertion( "GO:2000974") +AnnotationAssertion(rdfs:label "negative regulation of pro-B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of pro-B cell differentiation) + +AnnotationAssertion( "GO:2000975") +AnnotationAssertion(rdfs:label "positive regulation of pro-B cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of response to drug) + +AnnotationAssertion( "GO:2001023") +AnnotationAssertion(rdfs:label "regulation of response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of response to drug) + +AnnotationAssertion( "GO:2001024") +AnnotationAssertion(rdfs:label "negative regulation of response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of response to drug) + +AnnotationAssertion( "GO:2001025") +AnnotationAssertion(rdfs:label "positive regulation of response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of cellular response to drug) + +AnnotationAssertion( "GO:2001038") +AnnotationAssertion(rdfs:label "regulation of cellular response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cellular response to drug) + +AnnotationAssertion( "GO:2001039") +AnnotationAssertion(rdfs:label "negative regulation of cellular response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cellular response to drug) + +AnnotationAssertion( "GO:2001040") +AnnotationAssertion(rdfs:label "positive regulation of cellular response to drug") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (reactive nitrogen species metabolic process) + +AnnotationAssertion( "GO:2001057") +AnnotationAssertion(rdfs:label "reactive nitrogen species metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of RNA biosynthetic process) + +AnnotationAssertion( "GO:2001141") +AnnotationAssertion(rdfs:label "regulation of RNA biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of vasculogenesis) + +AnnotationAssertion( "GO:2001212") +AnnotationAssertion(rdfs:label "regulation of vasculogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of vasculogenesis) + +AnnotationAssertion( "GO:2001213") +AnnotationAssertion(rdfs:label "negative regulation of vasculogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of vasculogenesis) + +AnnotationAssertion( "GO:2001214") +AnnotationAssertion(rdfs:label "positive regulation of vasculogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of chromosome organization) + +AnnotationAssertion( "GO:2001251") +AnnotationAssertion(rdfs:label "negative regulation of chromosome organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of chromosome organization) + +AnnotationAssertion( "GO:2001252") +AnnotationAssertion(rdfs:label "positive regulation of chromosome organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (conditional specification) + +AnnotationAssertion( "conditional specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that specifies what should happen if the trigger condition is fulfilled."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "OBI_0000349"@en) +AnnotationAssertion(rdfs:label "conditional specification"@en) +SubClassOf( ) + +# Class: (measurement unit label) + +AnnotationAssertion( "measurement unit label"@en) +AnnotationAssertion( "Examples of measurement unit labels are liters, inches, weight per volume."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) +AnnotationAssertion( "2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term."@en) +AnnotationAssertion( "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "measurement unit label"@en) +SubClassOf( ) + +# Class: (objective specification) + +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) +AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) +AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Barry Smith"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "goal specification"@en) +AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) +AnnotationAssertion( "OBI_0000217"@en) +AnnotationAssertion(rdfs:label "objective specification"@en) +SubClassOf( ) + +# Class: (action specification) + +AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion(rdfs:label "action specification"@en) +SubClassOf( ) + +# Class: (datum label) + +AnnotationAssertion( "datum label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) +AnnotationAssertion( "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion( "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. +") +AnnotationAssertion(rdfs:label "datum label"@en) +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion( "software"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit."@en) +AnnotationAssertion( "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "GROUP: OBI"@en) +AnnotationAssertion(rdfs:label "software"@en) +SubClassOf( ) + +# Class: (information carrier) + +AnnotationAssertion( "information carrier"@en) +AnnotationAssertion( "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A quality of an information bearer that imparts the information content"@en) +AnnotationAssertion( "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en) +AnnotationAssertion( "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "information carrier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: () + +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (scalar measurement datum) + +AnnotationAssertion( "10 feet. 3 ml."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en) +AnnotationAssertion( "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in +this case we explicitly refer to the singular form"@en) +AnnotationAssertion( "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "scalar measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectMinCardinality(1 )) +SubClassOf( DataMinCardinality(1 )) + +# Class: (directive information entity) + +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) +AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (dot plot) + +AnnotationAssertion( "dot plot"@en) +AnnotationAssertion( "Dot plot of SSC-H and FSC-H."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions."@en) +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000123"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "dot plot"@en) +SubClassOf( ) + +# Class: (graph) + +AnnotationAssertion( "graph"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "OBI_0000240"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "graph"@en) +SubClassOf( ) + +# Class: (rule) + +AnnotationAssertion( "rule"@en) +AnnotationAssertion( "example to be added"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A rule is an executable which guides, defines, restricts actions."@en) +AnnotationAssertion( "MSI"@en) +AnnotationAssertion( "PRS"@en) +AnnotationAssertion( "OBI_0500021"@en) +AnnotationAssertion( "PRS"@en) +AnnotationAssertion(rdfs:label "rule"@en) +SubClassOf( ) + +# Class: (algorithm) + +AnnotationAssertion( "algorithm"@en) +AnnotationAssertion( "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en) +AnnotationAssertion( "Philippe Rocca-Serra"@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI_0000270"@en) +AnnotationAssertion( "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en) +AnnotationAssertion(rdfs:label "algorithm"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (source code module) + +AnnotationAssertion( "source code module"@en) +AnnotationAssertion( "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000039"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "source code module"@en) +SubClassOf( ) + +# Class: (data format specification) + +AnnotationAssertion( "data format specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"@en) +AnnotationAssertion( "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file\""@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "OBI_0000187"@en) +AnnotationAssertion(rdfs:label "data format specification"@en) +SubClassOf( ) + +# Class: (data set) + +AnnotationAssertion( "data set"@en) +AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) +AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) +AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000042"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "data set"@en) +SubClassOf( ) + +# Class: (image) + +AnnotationAssertion( "image"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Allyson"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000030"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "image"@en) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) +AnnotationAssertion( "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231."@en) +AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Clint Dowland"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion( "OBI_0000344"@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (measurement datum) + +AnnotationAssertion( "measurement datum"@en) +AnnotationAssertion( "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en) +AnnotationAssertion( "2/2/2009 is_specified_output of some assay?"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000305"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (version number) + +AnnotationAssertion( "version number"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name."@en) +AnnotationAssertion( "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version"@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion(rdfs:label "version number"@en) +SubClassOf( ) + +# Class: (conclusion textual entity) + +AnnotationAssertion( "conclusion textual entity"@en) +AnnotationAssertion( "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers."@en) +AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) +AnnotationAssertion( "2009/10/23 Alan Ruttenberg: We need to work on the definition still"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "conclusion textual entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material information bearer) + +AnnotationAssertion( "material information bearer"@en) +AnnotationAssertion( "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier."@en) +AnnotationAssertion( "a brain"@en) +AnnotationAssertion( "a hard drive"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity in which a concretization of an information content entity inheres."@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion(rdfs:label "material information bearer"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (histogram) + +AnnotationAssertion( "histogram"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI"@en) +AnnotationAssertion(rdfs:label "histogram"@en) +SubClassOf( ) + +# Class: (heatmap) + +AnnotationAssertion( "heatmap"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI"@en) +AnnotationAssertion(rdfs:label "heatmap"@en) +SubClassOf( ) + +# Class: (dendrogram) + +AnnotationAssertion( "dendrogram"@en) +AnnotationAssertion( "Dendrograms are often used in computational biology to +illustrate the clustering of genes."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Dendrogram"@en) +AnnotationAssertion(rdfs:label "dendrogram"@en) +SubClassOf( ) + +# Class: (scatter plot) + +AnnotationAssertion( "scatter plot"@en) +AnnotationAssertion( "Comparison of gene expression values in two samples can be displayed in a scatter plot"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:James Malone"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "scattergraph"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Scatterplot"@en) +AnnotationAssertion(rdfs:label "scatter plot"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (textual entity) + +AnnotationAssertion( "textual entity"@en) +AnnotationAssertion( "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en) +AnnotationAssertion( "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en) +AnnotationAssertion( "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "text"@en) +AnnotationAssertion(rdfs:label "textual entity"@en) +SubClassOf( ) + +# Class: (table) + +AnnotationAssertion( "table"@en) +AnnotationAssertion( "| T F +--+----- +T | T F +F | F F"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "table"@en) +SubClassOf( ) + +# Class: (figure) + +AnnotationAssertion( "figure"@en) +AnnotationAssertion( "Any picture, diagram or table"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "figure"@en) +SubClassOf( ) + +# Class: (diagram) + +AnnotationAssertion( "diagram"@en) +AnnotationAssertion( "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A figure that expresses one or more propositions"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "diagram"@en) +SubClassOf( ) + +# Class: (document) + +AnnotationAssertion( "document"@en) +AnnotationAssertion( "A journal article, patent application, laboratory notebook, or a book"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "document"@en) +SubClassOf( ) + +# Class: (publication) + +AnnotationAssertion( "publication"@en) +AnnotationAssertion( "journal article, newspaper story, book, etc."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A document that is the output of a publishing process."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jie Zheng"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "published document"@en) +AnnotationAssertion(rdfs:label "publication"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (cartesian spatial coordinate datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude"@en) +AnnotationAssertion( "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "AR notes: We need to discuss whether it should include site.") +AnnotationAssertion(rdfs:label "cartesian spatial coordinate datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectExactCardinality(1 )) + +# Class: (one dimensional cartesian spatial coordinate datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "one dimensional cartesian spatial coordinate datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( DataExactCardinality(1 )) + +# Class: (two dimensional cartesian spatial coordinate datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "two dimensional cartesian spatial coordinate datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( DataExactCardinality(1 )) +SubClassOf( DataExactCardinality(1 )) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (mass measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum that is the result of measurement of mass quality"@en) +AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "mass measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectAllValuesFrom( ) ObjectAllValuesFrom( ))) + +# Class: (time measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum that is the result of measuring a temporal interval"@en) +AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "time measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectAllValuesFrom( ) ObjectAllValuesFrom( ))) + +# Class: (publishing process) + +AnnotationAssertion( ) +AnnotationAssertion( "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free."@en) +AnnotationAssertion( "Person: Jie Zheng"@en) +AnnotationAssertion( "https://en.wikipedia.org/wiki/Publishing") +AnnotationAssertion(rdfs:label "publishing process"@en) +SubClassOf( ) + +# Class: (documenting) + +AnnotationAssertion( "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A planned process in which a document is created or added to by including the specified input in it."@en) +AnnotationAssertion( "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape"@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) +AnnotationAssertion(rdfs:label "documenting"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (line graph) + +AnnotationAssertion( "line graph"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A line graph is a type of graph created by connecting a series of data +points together with a line."@en) +AnnotationAssertion( "PERSON:Chris Stoeckert"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "line chart"@en) +AnnotationAssertion( "GROUP:OBI"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Line_chart"@en) +AnnotationAssertion(rdfs:label "line graph"@en) +SubClassOf( ) + +# Class: (centrally registered identifier symbol) + +AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID symbol") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier symbol"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (centrally registered identifier) + +AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs."@en) +AnnotationAssertion( "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')."@en) +AnnotationAssertion( "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation."@en) +AnnotationAssertion( "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) + +# Class: (centrally registered identifier registry) + +AnnotationAssertion( "PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. "@en) +AnnotationAssertion( ) +AnnotationAssertion( "A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID registry") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier registry"@en) +SubClassOf( ) + +# Class: (time stamped measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time stamped measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (time sampled measurement data set) + +AnnotationAssertion( "pmid:20604925 - time-lapse live cell microscopy"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "experimental time series"@en) +AnnotationAssertion(rdfs:label "time sampled measurement data set"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (identifier) + +AnnotationAssertion( "identifier"@en) +AnnotationAssertion( "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "proper name"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:label "identifier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (identifier creating process) + +AnnotationAssertion( "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "dubbing process"@en) +AnnotationAssertion( "naming"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:label "identifier creating process"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (code set) + +AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "code map"@en) +AnnotationAssertion( "code system"@en) +AnnotationAssertion( "codeset"@en) +AnnotationAssertion( "coding system"@en) +AnnotationAssertion( "controlled vocabulary"@en) +AnnotationAssertion( "Alan Ruttenberg") +AnnotationAssertion( "Clint Dowland") +AnnotationAssertion( "Matt Diller") +AnnotationAssertion( "Sarah Bost") +AnnotationAssertion( "William R. Hogan") +AnnotationAssertion(rdfs:label "code set"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Proteomics Standards Initiative Mass Spectrometry Vocabularies) + +AnnotationAssertion( "MS:0000000") +AnnotationAssertion(rdfs:label "Proteomics Standards Initiative Mass Spectrometry Vocabularies") + +# Class: (standard) + +AnnotationAssertion( "MS:1000898") +AnnotationAssertion(rdfs:label "standard") +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (de facto standard) + +AnnotationAssertion( "MS:1000899") +AnnotationAssertion(rdfs:label "de facto standard") +SubClassOf( ) + +# Class: (minimum information standard) + +AnnotationAssertion( "MS:1000900") +AnnotationAssertion(rdfs:label "minimum information standard") +SubClassOf( ) + +# Class: (root) + +AnnotationAssertion( "NCBITaxon:1") +AnnotationAssertion(rdfs:label "root") +SubClassOf( ) + +# Class: (Muridae) + +AnnotationAssertion( "NCBITaxon:10066") +AnnotationAssertion(rdfs:label "Muridae") +SubClassOf( ) + +# Class: (Mus ) + +AnnotationAssertion( "NCBITaxon:10088") +AnnotationAssertion(rdfs:label "Mus ") +SubClassOf( ) + +# Class: (Mus musculus) + +AnnotationAssertion( "NCBITaxon:10090") +AnnotationAssertion(rdfs:label "Mus musculus") +SubClassOf( ) + +# Class: (Viruses) + +AnnotationAssertion( "NCBITaxon:10239") +AnnotationAssertion(rdfs:label "Viruses") +SubClassOf( ) + +# Class: (Cyanobacteriota) + +AnnotationAssertion( "NCBITaxon:1117") +AnnotationAssertion(rdfs:label "Cyanobacteriota") +SubClassOf( ) + +# Class: (Teleostomi) + +AnnotationAssertion( "NCBITaxon:117570") +AnnotationAssertion(rdfs:label "Teleostomi") +SubClassOf( ) + +# Class: (Euteleostomi) + +AnnotationAssertion( "NCBITaxon:117571") +AnnotationAssertion(rdfs:label "Euteleostomi") +SubClassOf( ) + +# Class: (cellular organisms) + +AnnotationAssertion( "NCBITaxon:131567") +AnnotationAssertion(rdfs:label "cellular organisms") +SubClassOf( ) + +# Class: (Dipnotetrapodomorpha) + +AnnotationAssertion( "NCBITaxon:1338369") +AnnotationAssertion(rdfs:label "Dipnotetrapodomorpha") +SubClassOf( ) + +# Class: (Eumycetozoa) + +AnnotationAssertion( "NCBITaxon:142796") +AnnotationAssertion(rdfs:label "Eumycetozoa") +SubClassOf( ) + +# Class: (Boreoeutheria) + +AnnotationAssertion( "NCBITaxon:1437010") +AnnotationAssertion(rdfs:label "Boreoeutheria") +SubClassOf( ) + +# Class: (Bacillati) + +AnnotationAssertion( "NCBITaxon:1783272") +AnnotationAssertion(rdfs:label "Bacillati") +SubClassOf( ) + +# Class: (Cyanobacteriota/Melainabacteria group) + +AnnotationAssertion( "NCBITaxon:1798711") +AnnotationAssertion(rdfs:label "Cyanobacteriota/Melainabacteria group") +SubClassOf( ) + +# Class: (Myomorpha) + +AnnotationAssertion( "NCBITaxon:1963758") +AnnotationAssertion(rdfs:label "Myomorpha") +SubClassOf( ) + +# Class: (Bacteria) + +AnnotationAssertion( "NCBITaxon:2") +AnnotationAssertion(rdfs:label "Bacteria") +SubClassOf( ) +DisjointClasses( ) + +# Class: (Dictyosteliaceae) + +AnnotationAssertion( "NCBITaxon:2058185") +AnnotationAssertion(rdfs:label "Dictyosteliaceae") +SubClassOf( ) + +# Class: (Dictyosteliales) + +AnnotationAssertion( "NCBITaxon:2058949") +AnnotationAssertion(rdfs:label "Dictyosteliales") +SubClassOf( ) + +# Class: (Homininae) + +AnnotationAssertion( "NCBITaxon:207598") +AnnotationAssertion(rdfs:label "Homininae") +SubClassOf( ) + +# Class: (Archaea) + +AnnotationAssertion( "NCBITaxon:2157") +AnnotationAssertion(rdfs:label "Archaea") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (Evosea) + +AnnotationAssertion( "NCBITaxon:2605435") +AnnotationAssertion(rdfs:label "Evosea") +SubClassOf( ) + +# Class: (Discoba) + +AnnotationAssertion( "NCBITaxon:2611352") +AnnotationAssertion(rdfs:label "Discoba") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (Eukaryota) + +AnnotationAssertion( "NCBITaxon:2759") +AnnotationAssertion(rdfs:label "Eukaryota") +SubClassOf( ) +DisjointClasses( ) + +# Class: (Euarchontoglires) + +AnnotationAssertion( "NCBITaxon:314146") +AnnotationAssertion(rdfs:label "Euarchontoglires") +SubClassOf( ) + +# Class: (Glires) + +AnnotationAssertion( "NCBITaxon:314147") +AnnotationAssertion(rdfs:label "Glires") +SubClassOf( ) + +# Class: (Simiiformes) + +AnnotationAssertion( "NCBITaxon:314293") +AnnotationAssertion(rdfs:label "Simiiformes") +SubClassOf( ) + +# Class: (Hominoidea) + +AnnotationAssertion( "NCBITaxon:314295") +AnnotationAssertion(rdfs:label "Hominoidea") +SubClassOf( ) + +# Class: (Tetrapoda) + +AnnotationAssertion( "NCBITaxon:32523") +AnnotationAssertion(rdfs:label "Tetrapoda") +SubClassOf( ) + +# Class: (Amniota) + +AnnotationAssertion( "NCBITaxon:32524") +AnnotationAssertion(rdfs:label "Amniota") +SubClassOf( ) + +# Class: (Theria ) + +AnnotationAssertion( "NCBITaxon:32525") +AnnotationAssertion(rdfs:label "Theria ") +SubClassOf( ) + +# Class: (Dictyostelia) + +AnnotationAssertion( "NCBITaxon:33083") +AnnotationAssertion(rdfs:label "Dictyostelia") +SubClassOf( ) + +# Class: (Viridiplantae) + +AnnotationAssertion( "NCBITaxon:33090") +AnnotationAssertion(rdfs:label "Viridiplantae") +SubClassOf( ) + +# Class: (Opisthokonta) + +AnnotationAssertion( "NCBITaxon:33154") +AnnotationAssertion(rdfs:label "Opisthokonta") +SubClassOf( ) + +# Class: (Metazoa) + +AnnotationAssertion( "NCBITaxon:33208") +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (Bilateria) + +AnnotationAssertion( "NCBITaxon:33213") +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Deuterostomia) + +AnnotationAssertion( "NCBITaxon:33511") +AnnotationAssertion(rdfs:label "Deuterostomia") +SubClassOf( ) + +# Class: (Euglenozoa) + +AnnotationAssertion( "NCBITaxon:33682") +AnnotationAssertion(rdfs:label "Euglenozoa") +SubClassOf( ) + +# Class: (Muroidea) + +AnnotationAssertion( "NCBITaxon:337687") +AnnotationAssertion(rdfs:label "Muroidea") +SubClassOf( ) + +# Class: (Haplorrhini) + +AnnotationAssertion( "NCBITaxon:376913") +AnnotationAssertion(rdfs:label "Haplorrhini") +SubClassOf( ) + +# Class: (Murinae) + +AnnotationAssertion( "NCBITaxon:39107") +AnnotationAssertion(rdfs:label "Murinae") +SubClassOf( ) + +# Class: (Mammalia) + +AnnotationAssertion( "NCBITaxon:40674") +AnnotationAssertion(rdfs:label "Mammalia") +SubClassOf( ) + +# Class: (Fungi) + +AnnotationAssertion( "NCBITaxon:4751") +AnnotationAssertion(rdfs:label "Fungi") +SubClassOf( ) + +# Class: (Amoebozoa) + +AnnotationAssertion( "NCBITaxon:554915") +AnnotationAssertion(rdfs:label "Amoebozoa") +SubClassOf( ) +DisjointClasses( ) + +# Class: (Dictyostelium) + +AnnotationAssertion( "NCBITaxon:5782") +AnnotationAssertion(rdfs:label "Dictyostelium") +SubClassOf( ) + +# Class: (Eumetazoa) + +AnnotationAssertion( "NCBITaxon:6072") +AnnotationAssertion(rdfs:label "Eumetazoa") +SubClassOf( ) + +# Class: (Chordata) + +AnnotationAssertion( "NCBITaxon:7711") +AnnotationAssertion(rdfs:label "Chordata") +SubClassOf( ) + +# Class: (Vertebrata ) + +AnnotationAssertion( "NCBITaxon:7742") +AnnotationAssertion(rdfs:label "Vertebrata ") +SubClassOf( ) + +# Class: (Gnathostomata ) + +AnnotationAssertion( "NCBITaxon:7776") +AnnotationAssertion(rdfs:label "Gnathostomata ") +SubClassOf( ) + +# Class: (Sarcopterygii) + +AnnotationAssertion( "NCBITaxon:8287") +AnnotationAssertion(rdfs:label "Sarcopterygii") +SubClassOf( ) + +# Class: (Mus ) + +AnnotationAssertion( "NCBITaxon:862507") +AnnotationAssertion(rdfs:label "Mus ") +SubClassOf( ) + +# Class: (Craniata ) + +AnnotationAssertion( "NCBITaxon:89593") +AnnotationAssertion(rdfs:label "Craniata ") +SubClassOf( ) + +# Class: (Eutheria) + +AnnotationAssertion( "NCBITaxon:9347") +AnnotationAssertion(rdfs:label "Eutheria") +SubClassOf( ) + +# Class: (Primates) + +AnnotationAssertion( "NCBITaxon:9443") +AnnotationAssertion(rdfs:label "Primates") +SubClassOf( ) + +# Class: (Catarrhini) + +AnnotationAssertion( "NCBITaxon:9526") +AnnotationAssertion(rdfs:label "Catarrhini") +SubClassOf( ) + +# Class: (Hominidae) + +AnnotationAssertion( "NCBITaxon:9604") +AnnotationAssertion(rdfs:label "Hominidae") +SubClassOf( ) + +# Class: (Homo) + +AnnotationAssertion( "NCBITaxon:9605") +AnnotationAssertion(rdfs:label "Homo") +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion( "human being") +AnnotationAssertion( "NCBITaxon:9606") +AnnotationAssertion(rdfs:label "Homo sapiens") +SubClassOf( ) + +# Class: (Rodentia) + +AnnotationAssertion( "NCBITaxon:9989") +AnnotationAssertion(rdfs:label "Rodentia") +SubClassOf( ) + +# Class: (Viridiplantae or Bacteria) + +AnnotationAssertion(rdfs:label "Viridiplantae or Bacteria") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (Viridiplantae or Cyanobacteria) + +AnnotationAssertion(rdfs:label "Viridiplantae or Cyanobacteria") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Prokaryota) + +AnnotationAssertion(rdfs:label "Prokaryota") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (Viridiplantae or Archaea or Bacteria) + +AnnotationAssertion(rdfs:label "Viridiplantae or Archaea or Bacteria") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Viridiplantae or Bacteria or Euglenozoa) + +AnnotationAssertion(rdfs:label "Viridiplantae or Bacteria or Euglenozoa") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Viridiplantae or Euglenozoa) + +AnnotationAssertion(rdfs:label "Viridiplantae or Euglenozoa") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) + +# Class: (Fungi or Bacteria) + +AnnotationAssertion(rdfs:label "Fungi or Bacteria") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Viridiplantae or Bacteria or Euglenozoa or Archaea) + +AnnotationAssertion(rdfs:label "Viridiplantae or Bacteria or Euglenozoa or Archaea") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +DisjointClasses( ) + +# Class: (Fungi or Dictyostelium) + +AnnotationAssertion(rdfs:label "Fungi or Dictyostelium") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Fungi or Bacteria or Archaea) + +AnnotationAssertion(rdfs:label "Fungi or Bacteria or Archaea") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Unikonta) + +AnnotationAssertion(rdfs:label "Unikonta") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (Archaea or Eukaryota) + +AnnotationAssertion(rdfs:label "Archaea or Eukaryota") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (cellular organisms or viruses) + +AnnotationAssertion(rdfs:label "cellular organisms or viruses") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (planned process) + +AnnotationAssertion( "planned process") +AnnotationAssertion( "planned process"@en) +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "planned process"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (regulator role) + +AnnotationAssertion( "regulator role") +AnnotationAssertion( "Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders"@en) +AnnotationAssertion( "Person:Jennifer Fostel"@en) +AnnotationAssertion( "regulator") +AnnotationAssertion( "OBI"@en) +AnnotationAssertion(rdfs:label "regulator role"@en) +SubClassOf( ) + +# Class: (regulatory role) + +AnnotationAssertion( "regulatory role"@en) +AnnotationAssertion( "Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body."@en) +AnnotationAssertion( "GROUP: Role branch"@en) +AnnotationAssertion( "OBI, CDISC"@en) +AnnotationAssertion( "govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent"@en) +AnnotationAssertion(rdfs:label "regulatory role"@en) +SubClassOf( ) + +# Class: (material supplier role) + +AnnotationAssertion( "material supplier role") +AnnotationAssertion( "Jackson Labs is an organization which provide mice as experimental material") +AnnotationAssertion( ) +AnnotationAssertion( "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation."@en) +AnnotationAssertion( "Supplier role is a special kind of service, e.g. biobank") +AnnotationAssertion( "PERSON:Jennifer Fostel"@en) +AnnotationAssertion( "material provider role") +AnnotationAssertion( "supplier") +AnnotationAssertion(rdfs:label "material supplier role"@en) +SubClassOf( ) + +# Class: (classified data set) + +AnnotationAssertion( "classified data set") +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Monnie McGee") +AnnotationAssertion( "data set with assigned class labels") +AnnotationAssertion(rdfs:label "classified data set"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (chromatography column) + +AnnotationAssertion( "chromatography column") +AnnotationAssertion( ) +AnnotationAssertion( "Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Column_chromatography") +AnnotationAssertion( "open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178") +AnnotationAssertion(rdfs:label "chromatography column") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectAllValuesFrom( )))) + +# Class: (processed material) + +AnnotationAssertion( "processed material"@en) +AnnotationAssertion( "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Is a material entity that is created or changed during material processing."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "processed material"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (chromatography device) + +AnnotationAssertion( "chromatography device") +AnnotationAssertion( ) +AnnotationAssertion( "A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a \"mobile phase\" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "chromatography instrument") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Chromatography") +AnnotationAssertion( "open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178") +AnnotationAssertion(rdfs:label "chromatography device") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mass spectrometer) + +AnnotationAssertion( "mass spectrometer") +AnnotationAssertion( "LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific") +AnnotationAssertion( ) +AnnotationAssertion( "A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum"@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Mass_spectrometry") +AnnotationAssertion(rdfs:label "mass spectrometer") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (investigation) + +AnnotationAssertion( "investigation"@en) +AnnotationAssertion( "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "Could add specific objective specification"@en) +AnnotationAssertion( "Following OBI call November 2012,26th: it was decided there was no need for adding achieves objective of drawing conclusion as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "investigation"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (evaluant role) + +AnnotationAssertion( "evaluant role"@en) +AnnotationAssertion( "When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source."@en) +AnnotationAssertion( ) +AnnotationAssertion( "a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role"@en) +AnnotationAssertion( "Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)"@en) +AnnotationAssertion( "examples of features that could be described in an evaluant: quality.... e.g. \"contains 10 pg/ml IL2\", or \"no glucose detected\")"@en) +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion( "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.") +AnnotationAssertion(rdfs:label "evaluant role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: () + +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (culture medium) + +AnnotationAssertion( "culture medium") +AnnotationAssertion( "A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a processed material that provides the needed nourishment for microorganisms or cells grown in vitro."@en) +AnnotationAssertion( "changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 +Modification made by JZ.") +AnnotationAssertion( "Person: Jennifer Fostel, Jie Zheng"@en) +AnnotationAssertion( "OBI"@en) +AnnotationAssertion(rdfs:label "culture medium"@en) +SubClassOf( ) + +# Class: (reagent role) + +AnnotationAssertion( "reagent role") +AnnotationAssertion( "Buffer, dye, a catalyst, a solvating agent."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer."@en) +AnnotationAssertion( "PERSON:Matthew Brush"@en) +AnnotationAssertion( "reagent") +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion( "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + +May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities (\"a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances\"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.") +AnnotationAssertion(rdfs:label "reagent role"@en) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion( "material processing") +AnnotationAssertion( "A cell lysis, production of a cloning vector, creating a buffer.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process which results in physical changes in a specified input material"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca Serra") +AnnotationAssertion( "material transformation"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "material processing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (specimen role) + +AnnotationAssertion( "specimen role") +AnnotationAssertion( "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen."@en) +AnnotationAssertion( "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen."@en) +AnnotationAssertion( "parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject."@en) +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "specimen role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (investigation agent role) + +AnnotationAssertion( "investigation agent role") +AnnotationAssertion( "The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing."@en) +AnnotationAssertion( "Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.") +AnnotationAssertion( "Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)") +AnnotationAssertion( "GROUP: Role Branch"@en) +AnnotationAssertion( "investigator") +AnnotationAssertion( "OBI"@en) +AnnotationAssertion( "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.") +AnnotationAssertion(rdfs:label "investigation agent role") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organization) + +AnnotationAssertion( "organization"@en) +AnnotationAssertion( "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) +AnnotationAssertion( "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "PERSON: Susanna Sansone") +AnnotationAssertion( "GROUP: OBI") +AnnotationAssertion(rdfs:label "organization"@en) +SubClassOf( ) + +# Class: (protocol) + +AnnotationAssertion( "protocol"@en) +AnnotationAssertion( "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)"@en) +AnnotationAssertion(rdfs:label "protocol"@en) +SubClassOf( ) + +# Class: (eluate) + +AnnotationAssertion( "eluate"@en) +AnnotationAssertion( "Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase"@en) +AnnotationAssertion( "need to add restriction to indicate: has_part some (material entity has_role mobile phase) +need to add mobile phase as role"@en) +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "eluted material"@en) +AnnotationAssertion( "OBI Bionaterial") +AnnotationAssertion(rdfs:label "eluate"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (drawing a conclusion based on data) + +AnnotationAssertion( "interpreting data") +AnnotationAssertion( "Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "drawing a conclusion based on data"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (planning) + +AnnotationAssertion( "planning") +AnnotationAssertion( "The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a \"robot scientist\" executing software.") +AnnotationAssertion( ) +AnnotationAssertion( "a process of creating or modifying a plan specification"@en) +AnnotationAssertion( "7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Plans and Planned Processes Branch") +AnnotationAssertion(rdfs:label "planning"@en) +SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (mass analyzer) + +AnnotationAssertion( "mass analyzer") +AnnotationAssertion( "The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation") +AnnotationAssertion( ) +AnnotationAssertion( "A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "PERSON: Daniel Schober") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer") +AnnotationAssertion(rdfs:label "mass analyzer") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ion source) + +AnnotationAssertion( "ion source") +AnnotationAssertion( "The ion source of a Voyager-DE??? STR Biospectrometry Workstation") +AnnotationAssertion( ) +AnnotationAssertion( "An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9)))."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source") +AnnotationAssertion(rdfs:label "ion source") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ion detector) + +AnnotationAssertion( "ion detector") +AnnotationAssertion( "The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation") +AnnotationAssertion( ) +AnnotationAssertion( "An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Mass_spectrometry#Detector") +AnnotationAssertion(rdfs:label "ion detector") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (contain function) + +AnnotationAssertion( "contain function"@en) +AnnotationAssertion( "A syringe, a beaker") +AnnotationAssertion( ) +AnnotationAssertion( "A contain function is a function to constrain a material entities location in space"@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "contain function"@en) +SubClassOf( ) + +# Class: (heat function) + +AnnotationAssertion( "heat function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A heat function is a function that increases the internal kinetic energy of a material"@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "heat function"@en) +SubClassOf( ) + +# Class: (material separation function) + +AnnotationAssertion( "material separation function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality."@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "material separation function"@en) +SubClassOf( ) + +# Class: (ionization function) + +AnnotationAssertion( "ionization function"@en) +AnnotationAssertion( "The ion source in amass spectrometer") +AnnotationAssertion( ) +AnnotationAssertion( "An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions."@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Ionization"@en) +AnnotationAssertion(rdfs:label "ionization function"@en) +SubClassOf( ) + +# Class: (cool function) + +AnnotationAssertion( "cool function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material."@en) +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "cool function"@en) +SubClassOf( ) + +# Class: (environment control function) + +AnnotationAssertion( "environment control function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature."@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "environment control function"@en) +SubClassOf( ) + +# Class: (reverse transcriptase) + +AnnotationAssertion( "reverse transcriptase"@en) +AnnotationAssertion( ) +AnnotationAssertion( "enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase +activity)"@en) +AnnotationAssertion( "person:Melanie Courtot") +AnnotationAssertion( "group:OBI") +AnnotationAssertion(rdfs:label "reverse transcriptase"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectAllValuesFrom( )))) +SubClassOf( ) + +# Class: (enzyme) + +AnnotationAssertion( "enzyme"@en) +AnnotationAssertion( ) +AnnotationAssertion( "(protein or rna) or has_part (protein or rna) and +has_function some GO:0003824 (catalytic activity)"@en) +AnnotationAssertion( "MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything +that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.") +AnnotationAssertion( "person: Melanie Courtot") +AnnotationAssertion( "GROUP:OBI") +AnnotationAssertion(rdfs:label "enzyme"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectUnionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectAllValuesFrom( )))) +SubClassOf( ) + +# Class: (assay objective) + +AnnotationAssertion( "assay objective") +AnnotationAssertion( "the objective to determine the weight of a mouse.") +AnnotationAssertion( ) +AnnotationAssertion( "an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)"@en) +AnnotationAssertion( "PPPB branch") +AnnotationAssertion( "PPPB branch") +AnnotationAssertion(rdfs:label "assay objective"@en) +SubClassOf( ) + +# Class: (regulatory agency) + +AnnotationAssertion( "regulatory agency"@en) +AnnotationAssertion( "The US Environmental Protection Agency") +AnnotationAssertion( ) +AnnotationAssertion( "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government."@en) +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: en.wikipedia.org/wiki/Regulator") +AnnotationAssertion(rdfs:label "regulatory agency"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (normalized data set) + +AnnotationAssertion( "normalized data set") +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is produced as the output of a normalization data transformation."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion(rdfs:label "normalized data set"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (measure function) + +AnnotationAssertion( "measure function"@en) +AnnotationAssertion( "A glucometer measures blood glucose concentration, the glucometer has a measure function.") +AnnotationAssertion( ) +AnnotationAssertion( "Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference."@en) +AnnotationAssertion( "PERSON: Daniel Schober") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON:Frank Gibson") +AnnotationAssertion(rdfs:label "measure function"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( ObjectSomeValuesFrom( ))) + +# Class: (material transformation objective) + +AnnotationAssertion( "material transformation objective") +AnnotationAssertion( "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.") +AnnotationAssertion( ) +AnnotationAssertion( "an objective specifiction that creates an specific output object from input materials."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "artifact creation objective"@en) +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "material transformation objective"@en) +SubClassOf( ) + +# Class: (manufacturing) + +AnnotationAssertion( "manufacturing") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to produce a processed material which will have a function for future use."@en) +AnnotationAssertion( "A person or organization (having manufacturer role) is a participant in this process") +AnnotationAssertion( "Manufacturing implies reproducibility and responsibility AR") +AnnotationAssertion( "This includes a single scientist making a processed material for personal use."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (manufacturing objective) + +AnnotationAssertion( "manufacturing objective") +AnnotationAssertion( ) +AnnotationAssertion( "is the objective to manufacture a material of a certain function (device)"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing objective"@en) +SubClassOf( ) + +# Class: (mass spectrometry assay) + +AnnotationAssertion( "Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.") +AnnotationAssertion( "An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles."@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "mass spectrometry assay") +EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (study design execution) + +AnnotationAssertion( "study design execution") +AnnotationAssertion( "injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.") +AnnotationAssertion( ) +AnnotationAssertion( "a planned process that carries out a study design") +AnnotationAssertion( "a planned process that carries out a study design"@en) +AnnotationAssertion( "removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "study design execution") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (manufacturer role) + +AnnotationAssertion( "manufacturer role") +AnnotationAssertion( "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.") +AnnotationAssertion( ) +AnnotationAssertion( "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process."@en) +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "manufacturer role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (scattered molecular aggregate) + +AnnotationAssertion( "scattered molecular aggregate") +AnnotationAssertion( "the sodium and chloride ions in a glass of salt water") +AnnotationAssertion( ) +AnnotationAssertion( "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "Collective"@en) +AnnotationAssertion( "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"@en) +AnnotationAssertion(rdfs:label "scattered molecular aggregate"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (material separation objective) + +AnnotationAssertion( "material separation objective") +AnnotationAssertion( "The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.") +AnnotationAssertion( ) +AnnotationAssertion( "is an objective to transform a material entity into spatially separated components."@en) +AnnotationAssertion( "PPPB branch") +AnnotationAssertion( "PPPB branch") +AnnotationAssertion(rdfs:label "material separation objective") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (clustered data set) + +AnnotationAssertion( "clustered data set") +AnnotationAssertion( "A clustered data set is the output of a K means clustering data transformation") +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Monnie McGee") +AnnotationAssertion( "data set with assigned discovered class labels") +AnnotationAssertion( "AR thinks could be a data item instead") +AnnotationAssertion(rdfs:label "clustered data set"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (material combination) + +AnnotationAssertion( "material combination") +AnnotationAssertion( "Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.") +AnnotationAssertion( ) +AnnotationAssertion( "is a material processing with the objective to combine two or more material entities as input into a single material entity as output."@en) +AnnotationAssertion( "created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.") +AnnotationAssertion( "bp") +AnnotationAssertion( "bp") +AnnotationAssertion(rdfs:label "material combination") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (specimen collection process) + +AnnotationAssertion( "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed."@en) +AnnotationAssertion( "Definition updated following discussion on 2024-10-07 OBI dev call.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.") +AnnotationAssertion( "Philly2013: The specimen_role for the specimen is created during the specimen collection process.") +AnnotationAssertion( "label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "specimen collection") +AnnotationAssertion( "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession") +AnnotationAssertion( "6/9/09: used at workshop") +AnnotationAssertion(rdfs:label "specimen collection process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (class prediction data transformation) + +AnnotationAssertion( "class prediction data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "supervised classification data transformation") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "class prediction data transformation"@en) +EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (portioning objective) + +AnnotationAssertion( "portioning objective") +AnnotationAssertion( "The objective to obtain multiple aliquots of an enzyme preparation.") +AnnotationAssertion( ) +AnnotationAssertion( "A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material."@en) +AnnotationAssertion(rdfs:label "portioning objective") +SubClassOf( ) +DisjointClasses( ) + +# Class: (separation into different composition objective) + +AnnotationAssertion( "separation into different composition objective") +AnnotationAssertion( "The objective to obtain cells contained in a sample of blood.") +AnnotationAssertion( ) +AnnotationAssertion( "A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)."@en) +AnnotationAssertion( "We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives") +AnnotationAssertion(rdfs:label "separation into different composition objective") +SubClassOf( ) + +# Class: (specimen collection objective) + +AnnotationAssertion( "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed."@en) +AnnotationAssertion( "OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "specimen collection objective") +SubClassOf( ) + +# Class: (creating a mixture of molecules in solution) + +AnnotationAssertion( "creating a mixture of molecules in solution") +AnnotationAssertion( "The production of PBS") +AnnotationAssertion( ) +AnnotationAssertion( "is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion(rdfs:label "creating a mixture of molecules in solution") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material combination objective) + +AnnotationAssertion( "material combination objective") +AnnotationAssertion( ) +AnnotationAssertion( "is an objective to obtain an output material that contains several input materials."@en) +AnnotationAssertion( "PPPB branch") +AnnotationAssertion( "bp") +AnnotationAssertion(rdfs:label "material combination objective") +SubClassOf( ) + +# Class: (support vector machine) + +AnnotationAssertion( "support vector machine") +AnnotationAssertion( ) +AnnotationAssertion( "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion( "SVM") +AnnotationAssertion( "PERSON: Ryan Brinkman") +AnnotationAssertion(rdfs:label "support vector machine") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (decision tree induction objective) + +AnnotationAssertion( "decision tree induction objective") +AnnotationAssertion( ) +AnnotationAssertion( "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "decision tree induction objective") +SubClassOf( ) + +# Class: (decision tree building data transformation) + +AnnotationAssertion( "decision tree building data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A decision tree building data transformation is a data transformation that has objective decision tree induction."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "decision tree building data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (GenePattern software) + +AnnotationAssertion( "GenePattern software") +AnnotationAssertion( ) +AnnotationAssertion( "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Person:Helen Parkinson") +AnnotationAssertion( "WEB: http://www.broadinstitute.org/cancer/software/genepattern/") +AnnotationAssertion(rdfs:label "GenePattern software") +SubClassOf( ) + +# Class: (peak matching) + +AnnotationAssertion( "peak matching") +AnnotationAssertion( ) +AnnotationAssertion( "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold"@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion( "PERSON: Ryan Brinkman") +AnnotationAssertion(rdfs:label "peak matching") +SubClassOf( ) + +# Class: (k-nearest neighbors) + +AnnotationAssertion( "k-nearest neighbors"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "k-NN") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "k-nearest neighbors"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (CART) + +AnnotationAssertion( "CART"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "classification and regression trees") +AnnotationAssertion( "BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining."@en) +AnnotationAssertion(rdfs:label "CART"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (statistical model validation) + +AnnotationAssertion( "statistical model validation") +AnnotationAssertion( "Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia") +AnnotationAssertion( ) +AnnotationAssertion( "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set."@en) +AnnotationAssertion( "Helen Parkinson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29") +AnnotationAssertion(rdfs:label "statistical model validation") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (material maintenance objective) + +AnnotationAssertion( "material maintenance objective") +AnnotationAssertion( ) +AnnotationAssertion( "An objective specification maintains some or all of the qualities of a material over time."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion(rdfs:label "material maintenance objective") +SubClassOf( ) + +# Class: (primary structure of DNA macromolecule) + +AnnotationAssertion( "primary structure of DNA macromolecule") +AnnotationAssertion( ) +AnnotationAssertion( "a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues."@en) +AnnotationAssertion( "placeholder for SO") +AnnotationAssertion( "BP et al") +AnnotationAssertion(rdfs:label "primary structure of DNA macromolecule") +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (measurement device) + +AnnotationAssertion( "measurement device") +AnnotationAssertion( "A ruler, a microarray scanner, a Geiger counter.") +AnnotationAssertion( ) +AnnotationAssertion( "A device in which a measure function inheres."@en) +AnnotationAssertion( "GROUP:OBI Philly workshop") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "measurement device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (manufacturer) + +AnnotationAssertion( "manufacturer") +AnnotationAssertion( ) +AnnotationAssertion( "A person or organization that has a manufacturer role."@en) +AnnotationAssertion(rdfs:label "manufacturer") +EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material maintenance) + +AnnotationAssertion( "material maintenance") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to maintain some or all of the characteristics of an input material over time."@en) +AnnotationAssertion(rdfs:label "material maintenance") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (primary structure of RNA molecule) + +AnnotationAssertion( "primary structure of RNA molecule") +AnnotationAssertion( ) +AnnotationAssertion( "The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together"@en) +AnnotationAssertion( "Person:Bjoern Peters") +AnnotationAssertion(rdfs:label "primary structure of RNA molecule") +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material separation device) + +AnnotationAssertion( "material separation device") +AnnotationAssertion( "flow cytometer") +AnnotationAssertion( ) +AnnotationAssertion( "A device with a separation function realized in a planed process"@en) +AnnotationAssertion(rdfs:label "material separation device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (service provider role) + +AnnotationAssertion( "service provider role") +AnnotationAssertion( "Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.") +AnnotationAssertion( ) +AnnotationAssertion( "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person"@en) +AnnotationAssertion( "PERSON:Helen Parkinson") +AnnotationAssertion(rdfs:label "service provider role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (processed specimen) + +AnnotationAssertion( "processed specimen") +AnnotationAssertion( ) +AnnotationAssertion( "A specimen that has been intentionally physically modified."@en) +AnnotationAssertion( "A tissue sample that has been sliced and stained for a histology study.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "processed specimen") +EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf( ))) + +# Class: (categorical label) + +AnnotationAssertion( "categorical label") +AnnotationAssertion( "The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.") +AnnotationAssertion( ) +AnnotationAssertion( "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "categorical label") +SubClassOf( ) + +# Class: (container) + +AnnotationAssertion( "container") +AnnotationAssertion( ) +AnnotationAssertion( "A device that can be used to restrict the location of material entities over time"@en) +AnnotationAssertion( "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion(rdfs:label "container") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (device) + +AnnotationAssertion( "device") +AnnotationAssertion( "A voltmeter is a measurement device which is intended to perform some measure function.") +AnnotationAssertion( "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent."@en) +AnnotationAssertion( "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "instrument") +AnnotationAssertion( "OBI development call 2012-12-17.") +AnnotationAssertion(rdfs:label "device") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (dose) + +AnnotationAssertion( "dose") +AnnotationAssertion( "An organism has been injected 1ml of vaccine") +AnnotationAssertion( ) +AnnotationAssertion( "A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses."@en) +AnnotationAssertion(rdfs:label "dose") +SubClassOf( ) + +# Class: (questionnaire) + +AnnotationAssertion( "questionnaire") +AnnotationAssertion( ) +AnnotationAssertion( "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study."@en) +AnnotationAssertion( "JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. +JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not."@en) +AnnotationAssertion( "Need to clarify if this is a document or a directive information entity (or what their connection is))") +AnnotationAssertion( "PERSON: Jessica Turner"@en) +AnnotationAssertion( "Merriam-Webster"@en) +AnnotationAssertion(rdfs:label "questionnaire") +SubClassOf( ) + +# Class: (environmental control device) + +AnnotationAssertion( "environmental control device") +AnnotationAssertion( "A growth chamber is an environmental control device.") +AnnotationAssertion( ) +AnnotationAssertion( "An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity."@en) +AnnotationAssertion( "Helen Parkinson") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "environmental control device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))) + +# Class: (cell specimen) + +AnnotationAssertion( "cell specimen") +AnnotationAssertion( ) +AnnotationAssertion( "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture."@en) +AnnotationAssertion( "Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828") +AnnotationAssertion( "PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl") +AnnotationAssertion( "MO_612 cell") +AnnotationAssertion(rdfs:label "cell specimen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (specimen from organism) + +AnnotationAssertion( ) +AnnotationAssertion( "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert, Jie Zheng") +AnnotationAssertion( "tissue specimen") +AnnotationAssertion( "MO_954 organism_part") +AnnotationAssertion(rdfs:label "specimen from organism") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))))) + +# Class: (rate measurement datum) + +AnnotationAssertion( "rate measurement datum") +AnnotationAssertion( "The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.") +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum that represents the number of events occuring over a time interval"@en) +AnnotationAssertion( "PERSON: Bjoern Peters, Randi Vita") +AnnotationAssertion( "IEDB") +AnnotationAssertion(rdfs:label "rate measurement datum") +SubClassOf( ) + +# Class: (drawing a conclusion) + +AnnotationAssertion( "Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. +Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process in which new information is inferred from existing information."@en) +AnnotationAssertion(rdfs:label "drawing a conclusion") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (reagent) + +AnnotationAssertion( ) +AnnotationAssertion( "A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output."@en) +AnnotationAssertion( "2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.") +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion(rdfs:label "reagent"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (comment on investigation) + +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity that is about any of the aspects of an investigation worth noting"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert, Jie Zheng") +AnnotationAssertion( "NIAID GSCID-BRC metadata working group") +AnnotationAssertion(rdfs:label "comment on investigation"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) + +# Class: (conclusion based on data) + +AnnotationAssertion( "The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. +The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. \"13 is prime\".") +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is inferred from data."@en) +AnnotationAssertion( "In the Philly 2013 workshop, we recognized the limitations of \"conclusion textual entity\", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.") +AnnotationAssertion( "Group:2013 Philly Workshop group") +AnnotationAssertion( "Group:2013 Philly Workshop group") +AnnotationAssertion(rdfs:label "conclusion based on data") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell freezing medium) + +AnnotationAssertion( "cell freezing medium") +AnnotationAssertion( ) +AnnotationAssertion( "A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles."@en) +AnnotationAssertion( "PERSON: Matthew Brush") +AnnotationAssertion(rdfs:label "cell freezing medium"@en) +SubClassOf( ) + +# Class: (categorical value specification) + +AnnotationAssertion( ) +AnnotationAssertion( "A value specification that is specifies one category out of a fixed number of nominal categories"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "categorical value specification") +SubClassOf( ) + +# Class: (scalar value specification) + +AnnotationAssertion( ) +AnnotationAssertion( "A value specification that consists of two parts: a numeral and a unit label"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "scalar value specification") +SubClassOf( ) +SubClassOf( ObjectMinCardinality(1 )) +SubClassOf( DataMinCardinality(1 )) + +# Class: (value specification) + +AnnotationAssertion( "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass.") +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that specifies a value within a classification scheme or on a quantitative scale."@en) +AnnotationAssertion( "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.") +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "value specification") +SubClassOf( ) + +# Class: (sequence assembly name) + +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity that is used to denote a sequence assembly."@en) +AnnotationAssertion( "PERSON: Jie Zheng, Chris Stoeckert") +AnnotationAssertion( "NIAID GSCID-BRC metadata working group") +AnnotationAssertion(rdfs:label "sequence assembly name"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (cytometry assay) + +AnnotationAssertion( "An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.") +AnnotationAssertion( "An assay that counts and/or measures characteristics of cells."@en) +AnnotationAssertion( "IEDB") +AnnotationAssertion( "IEDB") +AnnotationAssertion(rdfs:label "cytometry assay") +EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) + +# Class: (collection of specimens) + +AnnotationAssertion( "collection of specimens"@en) +AnnotationAssertion( "Blood cells collected from multiple donors over the course of a study."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) +AnnotationAssertion( "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/") +AnnotationAssertion( "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion( "OBIB, OBI") +AnnotationAssertion(rdfs:label "collection of specimens"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (container with environmental control) + +AnnotationAssertion( "container with environmental control") +AnnotationAssertion( "a freezer. a humidity controlled box.") +AnnotationAssertion( ) +AnnotationAssertion( "A container with an environmental control function."@en) +AnnotationAssertion( "For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/") +AnnotationAssertion( "Chris Stoeckert") +AnnotationAssertion( "Duke Biobank, OBIB") +AnnotationAssertion(rdfs:label "container with environmental control") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (histologic grade according to AJCC 7th edition) + +AnnotationAssertion( "G1:Well differentiated") +AnnotationAssertion( "G4: Undifferentiated") +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "histologic grade according to AJCC 7th edition") +SubClassOf( ) + +# Class: (histologic grade according to the Fuhrman Nuclear Grading System) + +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Histologic Grade (Fuhrman Nuclear Grading System)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "histologic grade according to the Fuhrman Nuclear Grading System") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor) + +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a ovarian tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor according to a two-tier grading system) + +AnnotationAssertion( "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor according to a two-tier grading system") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor according to the World Health Organization) + +AnnotationAssertion( "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor according to the World Health Organization") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for colon and rectum according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread lung primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for colon and rectum according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for colon and rectum according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for colon according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: colon distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for colon according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: lung distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: kidney distant Metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: ovarian distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (clinical tumor stage group according to AJCC 7th edition) + +AnnotationAssertion( "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Clinical tumor stage group (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "clinical tumor stage group according to AJCC 7th edition") +SubClassOf( ) + +# Class: (International Federation of Gynecology and Obstetrics cervical cancer stage value specification) + +AnnotationAssertion( "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Clinical FIGO stage") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "International Federation of Gynecology and Obstetrics cervical cancer stage value specification") +SubClassOf( ) + +# Class: (International Federation of Gynecology and Obstetrics ovarian cancer stage value specification) + +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification") +SubClassOf( ) + +# Class: (performance status value specification) + +AnnotationAssertion( "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Performance Status Scale") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Performance_status") +AnnotationAssertion(rdfs:label "performance status value specification") +SubClassOf( ) + +# Class: (Eastern Cooperative Oncology Group score value specification) + +AnnotationAssertion( "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "ECOG score") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "Eastern Cooperative Oncology Group score value specification") +SubClassOf( ) + +# Class: (Karnofsky score vaue specification) + +AnnotationAssertion( "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Karnofsky Score") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "Karnofsky score vaue specification") +SubClassOf( ) + +# Class: (molecular label role) + +AnnotationAssertion( "molecular label role"@en) +AnnotationAssertion( "A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay."@en) +AnnotationAssertion( "MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). +JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743.") +AnnotationAssertion( "Group: OBI"@en) +AnnotationAssertion( "molecular tracer role"@en) +AnnotationAssertion( "OBI developer call, 3-12-12") +AnnotationAssertion(rdfs:label "molecular label role"@en) +SubClassOf( ) + +# Class: (molecular label) + +AnnotationAssertion( "molecular label"@en) +AnnotationAssertion( "A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay"@en) +AnnotationAssertion( "JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744."@en) +AnnotationAssertion( "Group: OBI"@en) +AnnotationAssertion( "molecular tracer"@en) +AnnotationAssertion( "OBI developer call, 3-12-12") +AnnotationAssertion(rdfs:label "molecular label"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material supplier) + +AnnotationAssertion( "material supplier") +AnnotationAssertion( "A person or organization that provides material supplies to other people or organizations."@en) +AnnotationAssertion( "Rebecca Jackson") +AnnotationAssertion(rdfs:label "material supplier") +EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (lymphocyte assay) + +AnnotationAssertion( "A cytometry assay that measures the abundance and/or characteristics of lymphocytes"@en) +AnnotationAssertion( "James A. Overton, ORCID:0000-0001-5139-5572") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "lymphocyte assay") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) + +# Class: (liquid chromatography mass spectrometry assay) + +AnnotationAssertion( "A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance."@en) +AnnotationAssertion( "Michelle Giglio") +AnnotationAssertion( "Rebecca Jackson") +AnnotationAssertion( "Suvarna Nadendla") +AnnotationAssertion( "LC-MS") +AnnotationAssertion( "CHMO:0000524") +AnnotationAssertion(rdfs:label "liquid chromatography mass spectrometry assay") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (tandem mass spectrometry assay) + +AnnotationAssertion( "A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.") +AnnotationAssertion( "A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules)."@en) +AnnotationAssertion( "Discussed on the OBI developer call 2022-03-07: 'tandem mass spectrometry' OBI:0200198 is under 'data transformation' but is actually defined like an assay. Moving OBI:0200198 from 'data transformation' to 'assay' is a major logical change, so the OBI development team supports obsoleting 'tandem mass spectrometry' OBI:0200198 and replacing it with ‘tandem mass spectrometry assay’ OBI:0003540.") +AnnotationAssertion( "Hector Guzman-Orozco, ORCID:0000-0003-3430-8997") +AnnotationAssertion( "http://purl.obolibrary.org/obo/OBI_0200198") +AnnotationAssertion(rdfs:label "tandem mass spectrometry assay") +SubClassOf( ) + +# Class: (liquid chromatography) + +AnnotationAssertion( "A preparative chromatography in which material components are separated in a liquid solution."@en) +AnnotationAssertion( "Hector Guzman-Orozco") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "liquid chromatography") +SubClassOf( ) + +# Class: (cell culture assay) + +AnnotationAssertion( "An assay that has cell culture as an input."@en) +AnnotationAssertion( "Randi Vita") +AnnotationAssertion( "Sebastian Duesing") +AnnotationAssertion(rdfs:label "cell culture assay") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (reactant role) + +AnnotationAssertion( "A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction."@en) +AnnotationAssertion( "Sebastian Duesing") +AnnotationAssertion(rdfs:label "reactant role"@en) +SubClassOf( ) + +# Class: (Epstein Barr virus transformed B cell) + +AnnotationAssertion( "Epstein Barr virus transformed B cell"@en) +AnnotationAssertion( "PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity"@en) +AnnotationAssertion( "PERSON: Susanna Sansone") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion(rdfs:label "Epstein Barr virus transformed B cell"@en) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (specimen) + +AnnotationAssertion( "specimen"@en) +AnnotationAssertion( "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is collected for potential use as an input upon which measurements or observations are performed."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch"@en) +AnnotationAssertion(rdfs:label "specimen"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (cultured cell population) + +AnnotationAssertion( "cultured cell population") +AnnotationAssertion( "A cultured cell population applied in an experiment: \"293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest.\" (Lee, Ramee, et al. \"Regulation of cell survival by secreted proneurotrophins.\" Science 294.5548 (2001): 1945-1948). + +A cultured cell population maintained in vitro: \"Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks\" (Dichter, Marc A. \"Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation.\" Brain Research 149.2 (1978): 279-293).") +AnnotationAssertion( ) +AnnotationAssertion( "A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history."@en) +AnnotationAssertion( "2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line."@en) +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion( "cell culture sample") +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion(rdfs:label "cultured cell population") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (data transformation) + +AnnotationAssertion( "data transformation"@en) +AnnotationAssertion( "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process that produces output data from input data."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "Helen Parkinson"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "Richard Scheuermann"@en) +AnnotationAssertion( "Ryan Brinkman"@en) +AnnotationAssertion( "Tina Hernandez-Boussard"@en) +AnnotationAssertion( "data analysis"@en) +AnnotationAssertion( "data processing"@en) +AnnotationAssertion( "Branch editors"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (leave one out cross validation method) + +AnnotationAssertion( "leave one out cross validation method"@en) +AnnotationAssertion( "The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368") +AnnotationAssertion( ) +AnnotationAssertion( "is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data"@en) +AnnotationAssertion( "2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178") +AnnotationAssertion( "Person:Helen Parkinson") +AnnotationAssertion(rdfs:label "leave one out cross validation method"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (k-means clustering) + +AnnotationAssertion( "k-means clustering"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)."@en) +AnnotationAssertion( "Elisabetta Manduchi") +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/K-means"@en) +AnnotationAssertion(rdfs:label "k-means clustering"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hierarchical clustering) + +AnnotationAssertion( "hierarchical clustering"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering"@en) +AnnotationAssertion(rdfs:label "hierarchical clustering"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (dimensionality reduction) + +AnnotationAssertion( "dimensionality reduction"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "data projection") +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "dimensionality reduction"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (principal components analysis dimensionality reduction) + +AnnotationAssertion( "principal components analysis dimensionality reduction"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "pca data reduction"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "principal components analysis dimensionality reduction"@en) +SubClassOf( ) + +# Class: (data visualization) + +AnnotationAssertion( "data visualization") +AnnotationAssertion( "Generation of a heatmap from a microarray dataset") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Tina Boussard"@en) +AnnotationAssertion( "data encoding as image") +AnnotationAssertion( "visualization"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "PERSON: Tina Boussard"@en) +AnnotationAssertion( "Possible future hierarchy might include this: +information_encoding +>data_encoding +>>image_encoding") +AnnotationAssertion(rdfs:label "data visualization"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( ObjectUnionOf( ))) + +# Class: (data transformation objective) + +AnnotationAssertion( "data transformation objective"@en) +AnnotationAssertion( "normalize objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An objective specification to transformation input data into output data"@en) +AnnotationAssertion( "Modified definition in 2013 Philly OBI workshop") +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "data transformation objective"@en) +SubClassOf( ) + +# Class: (data normalization objective) + +AnnotationAssertion( "data normalization objective"@en) +AnnotationAssertion( "Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as \"quantile normalization\", according to the procedure described e.g. in PMID 12538238."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A normalization objective is a data transformation objective where the aim is to remove +systematic sources of variation to put the data on equal footing in order +to create a common base for comparisons."@en) +AnnotationAssertion( "Elisabetta Manduchi") +AnnotationAssertion( "Helen Parkinson") +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "data normalization objective"@en) +SubClassOf( ) + +# Class: (normalization data transformation) + +AnnotationAssertion( "normalization data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A normalization data transformation is a data transformation that has objective normalization."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "normalization data transformation"@en) +EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (partitioning data transformation) + +AnnotationAssertion( "partitioning data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A partitioning data transformation is a data transformation that has objective partitioning."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "partitioning data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (partitioning objective) + +AnnotationAssertion( "partitioning objective"@en) +AnnotationAssertion( "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set."@en) +AnnotationAssertion( "Elisabetta Manduchi") +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion(rdfs:label "partitioning objective"@en) +SubClassOf( ) + +# Class: (class discovery data transformation) + +AnnotationAssertion( "class discovery data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "clustering data transformation") +AnnotationAssertion( "unsupervised classification data transformation") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "class discovery data transformation"@en) +EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (class discovery objective) + +AnnotationAssertion( "class discovery objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "clustering objective") +AnnotationAssertion( "discriminant analysis objective"@en) +AnnotationAssertion( "unsupervised classification objective"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "class discovery objective"@en) +SubClassOf( ) + +# Class: (class prediction objective) + +AnnotationAssertion( "class prediction objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and +class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "classification objective") +AnnotationAssertion( "supervised classification objective"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "class prediction objective"@en) +SubClassOf( ) + +# Class: (cross validation objective) + +AnnotationAssertion( "cross validation objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "rotation estimation objective"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Cross_validation") +AnnotationAssertion(rdfs:label "cross validation objective"@en) +SubClassOf( ) + +# Class: (clustered data visualization) + +AnnotationAssertion( "clustered data visualization") +AnnotationAssertion( ) +AnnotationAssertion( "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "clustered data visualization") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (pool of specimens) + +AnnotationAssertion( "pool of specimens") +AnnotationAssertion( ) +AnnotationAssertion( "A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish."@en) +AnnotationAssertion( "check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "GROUP: CEBS") +AnnotationAssertion(rdfs:label "pool of specimens") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectAllValuesFrom( ))))) + +# Class: (chemical solution) + +AnnotationAssertion( "chemical solution"@en) +AnnotationAssertion( "PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "liquid chemical solution"@en) +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion(rdfs:label "chemical solution"@en) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ) + +# Class: (solvent role) + +AnnotationAssertion( "solvent role") +AnnotationAssertion( "PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors."@en) +AnnotationAssertion( ) +AnnotationAssertion( "solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation"@en) +AnnotationAssertion( "The class CHEBI:solvent is logically equivalent to this class, iff it is properly subsumed under the BFO:role branch. The label and textual definition of this CHEBI class are however misleadingly denoting the material entity that bears this role and not the role itself. The OBI modeling was needed as what is considered a solvent in a mixture can depend on the intent of the person creating the mixture. It would be great if this could be dealt with in CHEBI itself. See also https://github.com/obi-ontology/obi/issues/1771."@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)") +AnnotationAssertion(rdfs:label "solvent role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (solute role) + +AnnotationAssertion( "solute role") +AnnotationAssertion( "PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure."@en) +AnnotationAssertion( ) +AnnotationAssertion( "solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)") +AnnotationAssertion(rdfs:label "solute role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (dissolved material entity) + +AnnotationAssertion( "dissolved material entity") +AnnotationAssertion( "Salt molecules that have been mixed into water") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has been going through a process of being put into solution"@en) +AnnotationAssertion( "Person:Bjoern Peters") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "dissolved material entity"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) + +# Class: (extraction) + +AnnotationAssertion( "extraction") +AnnotationAssertion( "nucleic acid extraction using phenol chloroform") +AnnotationAssertion( ) +AnnotationAssertion( "A material separation in which a desired component of an input material is separated from the remainder"@en) +AnnotationAssertion( "Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. +'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future."@en) +AnnotationAssertion( "Person:Bjoern Peters") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "extraction"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (elution) + +AnnotationAssertion( "elution") +AnnotationAssertion( "PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13."@en) +AnnotationAssertion( ) +AnnotationAssertion( "the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "wordnet.princeton.edu/perl/webwn") +AnnotationAssertion(rdfs:label "elution"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (study design) + +AnnotationAssertion( "study design"@en) +AnnotationAssertion( "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") +AnnotationAssertion( "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."@en) +AnnotationAssertion( "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.") +AnnotationAssertion( "PERSON: Chris Stoeckert") +AnnotationAssertion( "experimental design"@en) +AnnotationAssertion( "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "study design"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material component separation) + +AnnotationAssertion( "material component separation"@en) +AnnotationAssertion( "Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a material processing in which components of an input material become segregated in space"@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "IEDB"@en) +AnnotationAssertion(rdfs:label "material component separation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (maintaining cell culture) + +AnnotationAssertion( "maintaining cell culture"@en) +AnnotationAssertion( "When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to keep cells alive in a defined environment outside of an organism."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "maintaining cell culture"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (establishing cell culture) + +AnnotationAssertion( "'establishing cell culture'") +AnnotationAssertion( ) +AnnotationAssertion( "a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line)."@en) +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion( "PERSON:Matthew Brush") +AnnotationAssertion(rdfs:label "establishing cell culture") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (preparative chromatography) + +AnnotationAssertion( "preparative chromatography"@en) +AnnotationAssertion( "The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides."@en) +AnnotationAssertion( ) +AnnotationAssertion( "the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity"@en) +AnnotationAssertion( "PERSON:Kevin Clancy; Bjoern Peters"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "preparative chromatography"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phenotype) + +AnnotationAssertion( "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species."@en) +AnnotationAssertion( "Albert Goldfain") +AnnotationAssertion( "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion( "creation date: 2010-07-19T11:13:49Z") +AnnotationAssertion(rdfs:label "phenotype") +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (mass) + +AnnotationAssertion( "mass") +AnnotationAssertion( ) +AnnotationAssertion( "PATO:0000125") +AnnotationAssertion(rdfs:label "mass") +SubClassOf( ) + +# Class: (physical quality) + +AnnotationAssertion( "physical quality") +AnnotationAssertion( ) +AnnotationAssertion( "PATO:0001018") +AnnotationAssertion(rdfs:label "physical quality") +SubClassOf( ) + +# Class: (physical object quality) + +AnnotationAssertion( "physical object quality") +AnnotationAssertion( ) +AnnotationAssertion( "PATO:0001241") +AnnotationAssertion(rdfs:label "physical object quality") +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular quality) + +AnnotationAssertion( "PATO:0001396") +AnnotationAssertion(rdfs:label "cellular quality") +SubClassOf( ) + +# Class: (cellular potency) + +AnnotationAssertion( "PATO:0001397") +AnnotationAssertion(rdfs:label "cellular potency") +SubClassOf( ) + +# Class: (unipotent) + +AnnotationAssertion( "PATO:0001400") +AnnotationAssertion(rdfs:label "unipotent") +SubClassOf( ) + +# Class: (oligopotent) + +AnnotationAssertion( "PATO:0001401") +AnnotationAssertion(rdfs:label "oligopotent") +SubClassOf( ) + +# Class: (multipotent) + +AnnotationAssertion( "PATO:0001402") +AnnotationAssertion(rdfs:label "multipotent") +SubClassOf( ) + +# Class: (nucleate quality) + +AnnotationAssertion( "PATO:0001404") +AnnotationAssertion(rdfs:label "nucleate quality") +SubClassOf( ) + +# Class: (mononucleate) + +AnnotationAssertion( "PATO:0001407") +AnnotationAssertion(rdfs:label "mononucleate") +SubClassOf( ) + +# Class: (nucleated) + +AnnotationAssertion( "PATO:0002505") +AnnotationAssertion(rdfs:label "nucleated") +SubClassOf( ) + +# Class: (high nuclear/cytoplasmic ratio) + +AnnotationAssertion( "PATO:0040072") +AnnotationAssertion(rdfs:label "high nuclear/cytoplasmic ratio") +SubClassOf( ) + +# Class: (anatomical structure quality) + +AnnotationAssertion( "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.") +AnnotationAssertion( "PATO:0070044") +AnnotationAssertion(rdfs:label "anatomical structure quality") +SubClassOf( ) + +# Class: (anatomical histological quality) + +AnnotationAssertion( "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.") +AnnotationAssertion( "PATO:0070045") +AnnotationAssertion(rdfs:label "anatomical histological quality") +SubClassOf( ) + +# Class: (neutrophillic) + +AnnotationAssertion( "PATO:0070046") +AnnotationAssertion(rdfs:label "neutrophillic") +SubClassOf( ) + +# Class: (protein) + +AnnotationAssertion( "antithrombin III is a protein") +AnnotationAssertion( "PR:000000001") +AnnotationAssertion(rdfs:label "protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (CD19 molecule) + +AnnotationAssertion( "PR:000001002") +AnnotationAssertion(rdfs:label "CD19 molecule") +SubClassOf( ) + +# Class: (CD34 molecule) + +AnnotationAssertion( "PR:000001003") +AnnotationAssertion(rdfs:label "CD34 molecule") +SubClassOf( ) + +# Class: (CD4 molecule) + +AnnotationAssertion( "PR:000001004") +AnnotationAssertion(rdfs:label "CD4 molecule") +SubClassOf( ) + +# Class: (integrin alpha with A domain) + +AnnotationAssertion( "PR:000001005") +AnnotationAssertion(rdfs:label "integrin alpha with A domain") +SubClassOf( ) + +# Class: (integrin alpha-M) + +AnnotationAssertion( "PR:000001012") +AnnotationAssertion(rdfs:label "integrin alpha-M") +SubClassOf( ) + +# Class: (CD3 subunit with immunoglobulin domain) + +AnnotationAssertion( "PR:000001018") +AnnotationAssertion(rdfs:label "CD3 subunit with immunoglobulin domain") +SubClassOf( ) + +# Class: (CD3 epsilon) + +AnnotationAssertion( "PR:000001020") +AnnotationAssertion(rdfs:label "CD3 epsilon") +SubClassOf( ) + +# Class: (neural cell adhesion molecule) + +AnnotationAssertion( "PR:000001022") +AnnotationAssertion(rdfs:label "neural cell adhesion molecule") +SubClassOf( ) + +# Class: (neural cell adhesion molecule NCAM) + +AnnotationAssertion( "PR:000001023") +AnnotationAssertion(rdfs:label "neural cell adhesion molecule NCAM") +SubClassOf( ) + +# Class: (neural cell adhesion molecule 1) + +AnnotationAssertion( "PR:000001024") +AnnotationAssertion(rdfs:label "neural cell adhesion molecule 1") +SubClassOf( ) + +# Class: (CD2 molecule) + +AnnotationAssertion( "PR:000001083") +AnnotationAssertion(rdfs:label "CD2 molecule") +SubClassOf( ) + +# Class: (T-cell surface glycoprotein CD8 alpha chain) + +AnnotationAssertion( "PR:000001084") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain") +SubClassOf( ) + +# Class: (membrane-spanning 4-domains subfamily A member 1) + +AnnotationAssertion( "PR:000001289") +AnnotationAssertion(rdfs:label "membrane-spanning 4-domains subfamily A member 1") +SubClassOf( ) + +# Class: (cadherin) + +AnnotationAssertion( "PR:000001327") +AnnotationAssertion(rdfs:label "cadherin") +SubClassOf( ) + +# Class: (cadherin-5) + +AnnotationAssertion( "PR:000001444") +AnnotationAssertion(rdfs:label "cadherin-5") +SubClassOf( ) + +# Class: (T-cell surface glycoprotein CD5) + +AnnotationAssertion( "PR:000001839") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD5") +SubClassOf( ) + +# Class: (interleukin-7 receptor subunit alpha) + +AnnotationAssertion( "PR:000001869") +AnnotationAssertion(rdfs:label "interleukin-7 receptor subunit alpha") +SubClassOf( ) + +# Class: (CD14 molecule) + +AnnotationAssertion( "PR:000001889") +AnnotationAssertion(rdfs:label "CD14 molecule") +SubClassOf( ) + +# Class: (paired box protein PAX-5) + +AnnotationAssertion( "PR:000001903") +AnnotationAssertion(rdfs:label "paired box protein PAX-5") +SubClassOf( ) + +# Class: (vascular endothelial growth factor receptor) + +AnnotationAssertion( "PR:000001971") +AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor") +SubClassOf( ) + +# Class: (vascular endothelial growth factor receptor 2) + +AnnotationAssertion( "PR:000002112") +AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2") +SubClassOf( ) + +# Class: (Ly-6-like protein) + +AnnotationAssertion( "PR:000002976") +AnnotationAssertion(rdfs:label "Ly-6-like protein") +SubClassOf( ) + +# Class: (lymphocyte antigen 6G) + +AnnotationAssertion( "PR:000002978") +AnnotationAssertion(rdfs:label "lymphocyte antigen 6G") +SubClassOf( ) + +# Class: (lymphocyte antigen 76 (mouse)) + +AnnotationAssertion( "PR:000002981") +AnnotationAssertion(rdfs:label "lymphocyte antigen 76 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA nucleotidylexotransferase) + +AnnotationAssertion( "PR:000006611") +AnnotationAssertion(rdfs:label "DNA nucleotidylexotransferase") +SubClassOf( ) + +# Class: (T-cell acute lymphocytic leukemia protein 1) + +AnnotationAssertion( "PR:000016043") +AnnotationAssertion(rdfs:label "T-cell acute lymphocytic leukemia protein 1") +SubClassOf( ) + +# Class: (amino acid chain) + +AnnotationAssertion( "PR:000018263") +AnnotationAssertion(rdfs:label "amino acid chain") +SubClassOf( ) +SubClassOf( ObjectMinCardinality(2 )) + +# Class: (integrin alpha) + +AnnotationAssertion( "PR:000025796") +AnnotationAssertion(rdfs:label "integrin alpha") +SubClassOf( ) + +# Class: (Mus musculus protein) + +AnnotationAssertion( "PR:000029032") +AnnotationAssertion(rdfs:label "Mus musculus protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Homo sapiens protein) + +AnnotationAssertion( "PR:000029067") +AnnotationAssertion(rdfs:label "Homo sapiens protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (eukaryotic protein) + +AnnotationAssertion( "PR:000036194") +AnnotationAssertion(rdfs:label "eukaryotic protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing molecular entity) + +AnnotationAssertion( "PR:000064867") +AnnotationAssertion(rdfs:label "protein-containing molecular entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD4 (human)) + +AnnotationAssertion( "PR:P01730") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD4 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD8 alpha chain (mouse)) + +AnnotationAssertion( "PR:P01731") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD8 alpha chain (human)) + +AnnotationAssertion( "PR:P01732") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA nucleotidylexotransferase (human)) + +AnnotationAssertion( "PR:P04053") +AnnotationAssertion(rdfs:label "DNA nucleotidylexotransferase (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (integrin alpha-M (mouse)) + +AnnotationAssertion( "PR:P05555") +AnnotationAssertion(rdfs:label "integrin alpha-M (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD5 (human)) + +AnnotationAssertion( "PR:P06127") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD5 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD4 (mouse)) + +AnnotationAssertion( "PR:P06332") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD4 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface antigen CD2 (human)) + +AnnotationAssertion( "PR:P06729") +AnnotationAssertion(rdfs:label "T-cell surface antigen CD2 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD3 epsilon chain (human)) + +AnnotationAssertion( "PR:P07766") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD3 epsilon chain (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monocyte differentiation antigen CD14 (human)) + +AnnotationAssertion( "PR:P08571") +AnnotationAssertion(rdfs:label "monocyte differentiation antigen CD14 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface antigen CD2 (mouse)) + +AnnotationAssertion( "PR:P08920") +AnnotationAssertion(rdfs:label "T-cell surface antigen CD2 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (DNA nucleotidylexotransferase (mouse)) + +AnnotationAssertion( "PR:P09838") +AnnotationAssertion(rdfs:label "DNA nucleotidylexotransferase (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (monocyte differentiation antigen CD14 (mouse)) + +AnnotationAssertion( "PR:P10810") +AnnotationAssertion(rdfs:label "monocyte differentiation antigen CD14 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (integrin alpha-M (human)) + +AnnotationAssertion( "PR:P11215") +AnnotationAssertion(rdfs:label "integrin alpha-M (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B-lymphocyte antigen CD20 (human)) + +AnnotationAssertion( "PR:P11836") +AnnotationAssertion(rdfs:label "B-lymphocyte antigen CD20 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD5 (mouse)) + +AnnotationAssertion( "PR:P13379") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD5 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (neural cell adhesion molecule 1 (human)) + +AnnotationAssertion( "PR:P13591") +AnnotationAssertion(rdfs:label "neural cell adhesion molecule 1 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (neural cell adhesion molecule 1 (mouse)) + +AnnotationAssertion( "PR:P13595") +AnnotationAssertion(rdfs:label "neural cell adhesion molecule 1 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B-lymphocyte antigen CD19 (human)) + +AnnotationAssertion( "A CD19 molecule that is encoded in the genome of human.") +AnnotationAssertion( "PR:P15391") +AnnotationAssertion(rdfs:label "B-lymphocyte antigen CD19 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (interleukin-7 receptor subunit alpha (human)) + +AnnotationAssertion( "PR:P16871") +AnnotationAssertion(rdfs:label "interleukin-7 receptor subunit alpha (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (interleukin-7 receptor subunit alpha (mouse)) + +AnnotationAssertion( "PR:P16872") +AnnotationAssertion(rdfs:label "interleukin-7 receptor subunit alpha (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell acute lymphocytic leukemia protein 1 (human)) + +AnnotationAssertion( "PR:P17542") +AnnotationAssertion(rdfs:label "T-cell acute lymphocytic leukemia protein 1 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B-lymphocyte antigen CD20 (mouse)) + +AnnotationAssertion( "PR:P19437") +AnnotationAssertion(rdfs:label "B-lymphocyte antigen CD20 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell acute lymphocytic leukemia protein 1 homolog (mouse)) + +AnnotationAssertion( "PR:P22091") +AnnotationAssertion(rdfs:label "T-cell acute lymphocytic leukemia protein 1 homolog (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (T-cell surface glycoprotein CD3 epsilon chain (mouse)) + +AnnotationAssertion( "PR:P22646") +AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD3 epsilon chain (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (B-lymphocyte antigen CD19 (mouse)) + +AnnotationAssertion( "PR:P25918") +AnnotationAssertion(rdfs:label "B-lymphocyte antigen CD19 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic progenitor cell antigen CD34 (human)) + +AnnotationAssertion( "A CD34 molecule that is encoded in the genome of human.") +AnnotationAssertion( "PR:P28906") +AnnotationAssertion(rdfs:label "hematopoietic progenitor cell antigen CD34 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cadherin-5 (human)) + +AnnotationAssertion( "PR:P33151") +AnnotationAssertion(rdfs:label "cadherin-5 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lymphocyte antigen 6G (mouse)) + +AnnotationAssertion( "PR:P35461") +AnnotationAssertion(rdfs:label "lymphocyte antigen 6G (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vascular endothelial growth factor receptor 2 (mouse)) + +AnnotationAssertion( "PR:P35918") +AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vascular endothelial growth factor receptor 2 (human)) + +AnnotationAssertion( "PR:P35968") +AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cadherin-5 (mouse)) + +AnnotationAssertion( "PR:P55284") +AnnotationAssertion(rdfs:label "cadherin-5 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (paired box protein Pax-5 (human)) + +AnnotationAssertion( "PR:Q02548") +AnnotationAssertion(rdfs:label "paired box protein Pax-5 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (paired box protein Pax-5 (mouse)) + +AnnotationAssertion( "PR:Q02650") +AnnotationAssertion(rdfs:label "paired box protein Pax-5 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hematopoietic progenitor cell antigen CD34 (mouse)) + +AnnotationAssertion( "PR:Q64314") +AnnotationAssertion(rdfs:label "hematopoietic progenitor cell antigen CD34 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (region) + +AnnotationAssertion( "primary structure of sequence macromolecule") +AnnotationAssertion( "sequence") +AnnotationAssertion( "SO:0000001") +AnnotationAssertion(rdfs:label "region") +SubClassOf( ) + +# Class: (protein_coding) + +AnnotationAssertion( "A gene which, when transcribed, can be translated into a protein.") +AnnotationAssertion( "SO:0000010") +AnnotationAssertion(rdfs:label "protein_coding") +SubClassOf( ) + +# Class: (sequence_feature) + +AnnotationAssertion( "SO:0000110") +AnnotationAssertion(rdfs:label "sequence_feature") +DisjointClasses( ) + +# Class: (primary_transcript) + +AnnotationAssertion( "SO:0000185") +AnnotationAssertion(rdfs:label "primary_transcript") +SubClassOf( ) + +# Class: (tRNA_primary_transcript) + +AnnotationAssertion( "SO:0000210") +AnnotationAssertion(rdfs:label "tRNA_primary_transcript") +SubClassOf( ) + +# Class: (mature_transcript) + +AnnotationAssertion( "SO:0000233") +AnnotationAssertion(rdfs:label "mature_transcript") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (tRNA) + +AnnotationAssertion( "SO:0000253") +AnnotationAssertion(rdfs:label "tRNA") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sequence_assembly) + +AnnotationAssertion( "SO:0000353") +AnnotationAssertion(rdfs:label "sequence_assembly") +SubClassOf( ) + +# Class: (sequence_attribute) + +AnnotationAssertion( "SO:0000400") +AnnotationAssertion(rdfs:label "sequence_attribute") + +# Class: (gene_attribute) + +AnnotationAssertion( "An attribute describing a gene.") +AnnotationAssertion( "SO:0000401") +AnnotationAssertion(rdfs:label "gene_attribute") +SubClassOf( ) + +# Class: (nc_primary_transcript) + +AnnotationAssertion( "SO:0000483") +AnnotationAssertion(rdfs:label "nc_primary_transcript") +SubClassOf( ) + +# Class: (ncRNA) + +AnnotationAssertion( "SO:0000655") +AnnotationAssertion(rdfs:label "ncRNA") +SubClassOf( ) + +# Class: (transcript) + +AnnotationAssertion( "SO:0000673") +AnnotationAssertion(rdfs:label "transcript") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gene) + +AnnotationAssertion( "SO:0000704") +AnnotationAssertion(rdfs:label "gene") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (feature_attribute) + +AnnotationAssertion( "SO:0000733") +AnnotationAssertion(rdfs:label "feature_attribute") +SubClassOf( ) + +# Class: (gene_member_region) + +AnnotationAssertion( "SO:0000831") +AnnotationAssertion(rdfs:label "gene_member_region") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein_coding_gene) + +AnnotationAssertion( "A gene that codes for an RNA that can be translated into a protein.") +AnnotationAssertion( "SO:0001217") +AnnotationAssertion(rdfs:label "protein_coding_gene") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (assembly) + +AnnotationAssertion( "SO:0001248") +AnnotationAssertion(rdfs:label "assembly") +SubClassOf( ) + +# Class: (experimental_feature) + +AnnotationAssertion( "SO:0001410") +AnnotationAssertion(rdfs:label "experimental_feature") +SubClassOf( ) + +# Class: (biological_region) + +AnnotationAssertion( "SO:0001411") +AnnotationAssertion(rdfs:label "biological_region") +SubClassOf( ) + +# Class: (sncRNA) + +AnnotationAssertion( "SO:0002247") +AnnotationAssertion(rdfs:label "sncRNA") +SubClassOf( ) + +# Class: (unit_of_gene_expression) + +AnnotationAssertion( "SO:0002300") +AnnotationAssertion(rdfs:label "unit_of_gene_expression") +SubClassOf( ) + +# Class: (gene_group) + +AnnotationAssertion( "SO:0005855") +AnnotationAssertion(rdfs:label "gene_group") +SubClassOf( ) + +# Class: () + +EquivalentClasses( ObjectHasSelf()) + +# Class: (unit) + +AnnotationAssertion(rdfs:label "unit") + +# Class: (length unit) + +AnnotationAssertion( "length unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (mass unit) + +AnnotationAssertion( "mass unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (time unit) + +AnnotationAssertion( "time unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (electric current unit) + +AnnotationAssertion(rdfs:label "electric current unit") +SubClassOf( ) + +# Class: (temperature unit) + +AnnotationAssertion(rdfs:label "temperature unit") +SubClassOf( ) + +# Class: (substance unit) + +AnnotationAssertion(rdfs:label "substance unit") +SubClassOf( ) + +# Class: (luminous intensity unit) + +AnnotationAssertion(rdfs:label "luminous intensity unit") +SubClassOf( ) + +# Class: (meter) + +AnnotationAssertion( "m") +AnnotationAssertion(rdfs:label "meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (kilogram) + +AnnotationAssertion( "kg") +AnnotationAssertion(rdfs:label "kilogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (second) + +AnnotationAssertion( "s") +AnnotationAssertion( "sec") +AnnotationAssertion(rdfs:label "second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (ampere) + +AnnotationAssertion(rdfs:label "ampere") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (kelvin) + +AnnotationAssertion(rdfs:label "kelvin") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (mole) + +AnnotationAssertion(rdfs:label "mole") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (candela) + +AnnotationAssertion(rdfs:label "candela") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (centimeter) + +AnnotationAssertion( "cm") +AnnotationAssertion(rdfs:label "centimeter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (millimeter) + +AnnotationAssertion( "mm") +AnnotationAssertion(rdfs:label "millimeter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (micrometer) + +AnnotationAssertion( "um") +AnnotationAssertion(rdfs:label "micrometer") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanometer) + +AnnotationAssertion( "nm") +AnnotationAssertion(rdfs:label "nanometer") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (angstrom) + +AnnotationAssertion(rdfs:label "angstrom") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (picometer) + +AnnotationAssertion(rdfs:label "picometer") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gram) + +AnnotationAssertion( "g") +AnnotationAssertion(rdfs:label "gram") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligram) + +AnnotationAssertion( "mg") +AnnotationAssertion(rdfs:label "milligram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microgram) + +AnnotationAssertion( "ug") +AnnotationAssertion(rdfs:label "microgram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanogram) + +AnnotationAssertion( "ng") +AnnotationAssertion(rdfs:label "nanogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picogram) + +AnnotationAssertion( "pg") +AnnotationAssertion(rdfs:label "picogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (femtogram) + +AnnotationAssertion(rdfs:label "femtogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (degree Celsius) + +AnnotationAssertion( "C") +AnnotationAssertion( "degree C") +AnnotationAssertion(rdfs:label "degree Celsius") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millisecond) + +AnnotationAssertion(rdfs:label "millisecond") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microsecond) + +AnnotationAssertion(rdfs:label "microsecond") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picosecond) + +AnnotationAssertion(rdfs:label "picosecond") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (minute) + +AnnotationAssertion( "min") +AnnotationAssertion(rdfs:label "minute") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (hour) + +AnnotationAssertion( "h") +AnnotationAssertion( "hr") +AnnotationAssertion(rdfs:label "hour") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (day) + +AnnotationAssertion(rdfs:label "day") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (week) + +AnnotationAssertion(rdfs:label "week") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (month) + +AnnotationAssertion(rdfs:label "month") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (year) + +AnnotationAssertion(rdfs:label "year") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milliampere) + +AnnotationAssertion(rdfs:label "milliampere") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microampere) + +AnnotationAssertion(rdfs:label "microampere") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (micromole) + +AnnotationAssertion( "umol") +AnnotationAssertion(rdfs:label "micromole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (millimole) + +AnnotationAssertion(rdfs:label "millimole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanomole) + +AnnotationAssertion( "nmol") +AnnotationAssertion(rdfs:label "nanomole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picomole) + +AnnotationAssertion( "pmol") +AnnotationAssertion(rdfs:label "picomole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (femtomole) + +AnnotationAssertion(rdfs:label "femtomole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (attomole) + +AnnotationAssertion(rdfs:label "attomole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (base unit) + +AnnotationAssertion(rdfs:label "base unit") +SubClassOf( ) + +# Class: (prefix) + +AnnotationAssertion(rdfs:label "prefix") + +# Class: (area unit) + +AnnotationAssertion(rdfs:label "area unit") +SubClassOf( ) + +# Class: (acceleration unit) + +AnnotationAssertion(rdfs:label "acceleration unit") +SubClassOf( ) + +# Class: (angular velocity unit) + +AnnotationAssertion(rdfs:label "angular velocity unit") +SubClassOf( ) + +# Class: (angular acceleration unit) + +AnnotationAssertion(rdfs:label "angular acceleration unit") +SubClassOf( ) + +# Class: (concentration unit) + +AnnotationAssertion(rdfs:label "concentration unit") +SubClassOf( ) + +# Class: (mass density unit) + +AnnotationAssertion(rdfs:label "mass density unit") +SubClassOf( ) + +# Class: (luminance unit) + +AnnotationAssertion(rdfs:label "luminance unit") +SubClassOf( ) + +# Class: (area density unit) + +AnnotationAssertion(rdfs:label "area density unit") +SubClassOf( ) + +# Class: (molar mass unit) + +AnnotationAssertion(rdfs:label "molar mass unit") +SubClassOf( ) + +# Class: (molar volume unit) + +AnnotationAssertion(rdfs:label "molar volume unit") +SubClassOf( ) + +# Class: (momentum unit) + +AnnotationAssertion(rdfs:label "momentum unit") +SubClassOf( ) + +# Class: (rotational frequency unit) + +AnnotationAssertion(rdfs:label "rotational frequency unit") +SubClassOf( ) + +# Class: (specific volume unit) + +AnnotationAssertion(rdfs:label "specific volume unit") +SubClassOf( ) + +# Class: (speed/velocity unit) + +AnnotationAssertion(rdfs:label "speed/velocity unit") +SubClassOf( ) + +# Class: (unit of molarity) + +AnnotationAssertion(rdfs:label "unit of molarity") +SubClassOf( ) + +# Class: (molar) + +AnnotationAssertion( "M") +AnnotationAssertion(rdfs:label "molar") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millimolar) + +AnnotationAssertion( "mM") +AnnotationAssertion(rdfs:label "millimolar") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (micromolar) + +AnnotationAssertion( "uM") +AnnotationAssertion(rdfs:label "micromolar") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanomolar) + +AnnotationAssertion( "nM") +AnnotationAssertion(rdfs:label "nanomolar") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picomolar) + +AnnotationAssertion( "pM") +AnnotationAssertion(rdfs:label "picomolar") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (unit of molality) + +AnnotationAssertion(rdfs:label "unit of molality") +SubClassOf( ) + +# Class: (molal) + +AnnotationAssertion(rdfs:label "molal") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millimolal) + +AnnotationAssertion(rdfs:label "millimolal") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (micromolal) + +AnnotationAssertion(rdfs:label "micromolal") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanomolal) + +AnnotationAssertion(rdfs:label "nanomolal") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picomolal) + +AnnotationAssertion(rdfs:label "picomolal") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (femtomolar) + +AnnotationAssertion(rdfs:label "femtomolar") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (unit of normality) + +AnnotationAssertion(rdfs:label "unit of normality") +SubClassOf( ) + +# Class: (normal) + +AnnotationAssertion(rdfs:label "normal") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mole fraction) + +AnnotationAssertion(rdfs:label "mole fraction") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (meter per second per second) + +AnnotationAssertion(rdfs:label "meter per second per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (radian per second per second) + +AnnotationAssertion(rdfs:label "radian per second per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (radian per second) + +AnnotationAssertion(rdfs:label "radian per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (square meter) + +AnnotationAssertion(rdfs:label "square meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (square centimeter) + +AnnotationAssertion(rdfs:label "square centimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (square millimeter) + +AnnotationAssertion(rdfs:label "square millimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilogram per cubic meter) + +AnnotationAssertion(rdfs:label "kilogram per cubic meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gram per cubic centimeter) + +AnnotationAssertion(rdfs:label "gram per cubic centimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (candela per square meter) + +AnnotationAssertion(rdfs:label "candela per square meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilogram per square meter) + +AnnotationAssertion(rdfs:label "kilogram per square meter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (kilogram per mole) + +AnnotationAssertion(rdfs:label "kilogram per mole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gram per mole) + +AnnotationAssertion(rdfs:label "gram per mole") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cubic meter per mole) + +AnnotationAssertion(rdfs:label "cubic meter per mole") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cubic centimeter per mole) + +AnnotationAssertion(rdfs:label "cubic centimeter per mole") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilogram meter per second) + +AnnotationAssertion(rdfs:label "kilogram meter per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (turns per second) + +AnnotationAssertion(rdfs:label "turns per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cubic meter per kilogram) + +AnnotationAssertion(rdfs:label "cubic meter per kilogram") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (meter per second) + +AnnotationAssertion(rdfs:label "meter per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (volume unit) + +AnnotationAssertion(rdfs:label "volume unit") +SubClassOf( ) + +# Class: (cubic meter) + +AnnotationAssertion(rdfs:label "cubic meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cubic centimeter) + +AnnotationAssertion( "cc") +AnnotationAssertion(rdfs:label "cubic centimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milliliter) + +AnnotationAssertion( "ml") +AnnotationAssertion(rdfs:label "milliliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (liter) + +AnnotationAssertion( "L") +AnnotationAssertion(rdfs:label "liter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cubic decimeter) + +AnnotationAssertion(rdfs:label "cubic decimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (microliter) + +AnnotationAssertion( "ul") +AnnotationAssertion(rdfs:label "microliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanoliter) + +AnnotationAssertion( "nl") +AnnotationAssertion(rdfs:label "nanoliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picoliter) + +AnnotationAssertion( "pl") +AnnotationAssertion(rdfs:label "picoliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (femtoliter) + +AnnotationAssertion(rdfs:label "femtoliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (frequency unit) + +AnnotationAssertion(rdfs:label "frequency unit") +SubClassOf( ) + +# Class: (hertz) + +AnnotationAssertion(rdfs:label "hertz") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (force unit) + +AnnotationAssertion(rdfs:label "force unit") +SubClassOf( ) + +# Class: (newton) + +AnnotationAssertion(rdfs:label "newton") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pressure unit) + +AnnotationAssertion(rdfs:label "pressure unit") +SubClassOf( ) + +# Class: (pascal) + +AnnotationAssertion(rdfs:label "pascal") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (energy unit) + +AnnotationAssertion(rdfs:label "energy unit") +SubClassOf( ) + +# Class: (joule) + +AnnotationAssertion(rdfs:label "joule") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (power unit) + +AnnotationAssertion(rdfs:label "power unit") +SubClassOf( ) + +# Class: (watt) + +AnnotationAssertion(rdfs:label "watt") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (illuminance unit) + +AnnotationAssertion(rdfs:label "illuminance unit") +SubClassOf( ) + +# Class: (lux) + +AnnotationAssertion(rdfs:label "lux") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (luminous flux unit) + +AnnotationAssertion(rdfs:label "luminous flux unit") +SubClassOf( ) + +# Class: (lumen) + +AnnotationAssertion(rdfs:label "lumen") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (catalytic activity unit) + +AnnotationAssertion(rdfs:label "catalytic activity unit") +SubClassOf( ) + +# Class: (katal) + +AnnotationAssertion(rdfs:label "katal") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (angle unit) + +AnnotationAssertion(rdfs:label "angle unit") +SubClassOf( ) + +# Class: (plane angle unit) + +AnnotationAssertion(rdfs:label "plane angle unit") +SubClassOf( ) + +# Class: (radian) + +AnnotationAssertion(rdfs:label "radian") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (solid angle unit) + +AnnotationAssertion(rdfs:label "solid angle unit") +SubClassOf( ) + +# Class: (steradian) + +AnnotationAssertion(rdfs:label "steradian") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (radiation unit) + +AnnotationAssertion(rdfs:label "radiation unit") +SubClassOf( ) + +# Class: (activity (of a radionuclide) unit) + +AnnotationAssertion(rdfs:label "activity (of a radionuclide) unit") +SubClassOf( ) + +# Class: (absorbed dose unit) + +AnnotationAssertion(rdfs:label "absorbed dose unit") +SubClassOf( ) + +# Class: (dose equivalent unit) + +AnnotationAssertion(rdfs:label "dose equivalent unit") +SubClassOf( ) + +# Class: (exposure unit) + +AnnotationAssertion(rdfs:label "exposure unit") +SubClassOf( ) + +# Class: (becquerel) + +AnnotationAssertion(rdfs:label "becquerel") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (curie) + +AnnotationAssertion(rdfs:label "curie") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gray) + +AnnotationAssertion(rdfs:label "gray") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (rad) + +AnnotationAssertion(rdfs:label "rad") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (roentgen) + +AnnotationAssertion(rdfs:label "roentgen") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (sievert) + +AnnotationAssertion(rdfs:label "sievert") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millisievert) + +AnnotationAssertion(rdfs:label "millisievert") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microsievert) + +AnnotationAssertion(rdfs:label "microsievert") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (Roentgen equivalent man) + +AnnotationAssertion(rdfs:label "Roentgen equivalent man") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (microgray) + +AnnotationAssertion(rdfs:label "microgray") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (milligray) + +AnnotationAssertion(rdfs:label "milligray") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanogray) + +AnnotationAssertion(rdfs:label "nanogray") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanosievert) + +AnnotationAssertion(rdfs:label "nanosievert") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (millicurie) + +AnnotationAssertion(rdfs:label "millicurie") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microcurie) + +AnnotationAssertion(rdfs:label "microcurie") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (disintegrations per minute) + +AnnotationAssertion(rdfs:label "disintegrations per minute") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (counts per minute) + +AnnotationAssertion(rdfs:label "counts per minute") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (nanosecond) + +AnnotationAssertion(rdfs:label "nanosecond") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (century) + +AnnotationAssertion(rdfs:label "century") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (half life) + +AnnotationAssertion(rdfs:label "half life") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (foot candle) + +AnnotationAssertion(rdfs:label "foot candle") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (irradiance unit) + +AnnotationAssertion(rdfs:label "irradiance unit") +SubClassOf( ) + +# Class: (watt per square meter) + +AnnotationAssertion(rdfs:label "watt per square meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (einstein per square meter per second) + +AnnotationAssertion(rdfs:label "einstein per square meter per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (light unit) + +AnnotationAssertion(rdfs:label "light unit") +SubClassOf( ) + +# Class: (watt per steradian per square meter) + +AnnotationAssertion(rdfs:label "watt per steradian per square meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (radiant intensity unit) + +AnnotationAssertion(rdfs:label "radiant intensity unit") +SubClassOf( ) + +# Class: (microeinstein per square meter per second) + +AnnotationAssertion(rdfs:label "microeinstein per square meter per second") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (radiance unit) + +AnnotationAssertion(rdfs:label "radiance unit") +SubClassOf( ) + +# Class: (watt per steradian) + +AnnotationAssertion(rdfs:label "watt per steradian") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mass percentage) + +AnnotationAssertion( "% w/w") +AnnotationAssertion( "percent weight pr weight") +AnnotationAssertion(rdfs:label "mass percentage") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mass volume percentage) + +AnnotationAssertion( "% w/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion(rdfs:label "mass volume percentage") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (volume percentage) + +AnnotationAssertion( "% v/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion(rdfs:label "volume percentage") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per notation unit) + +AnnotationAssertion(rdfs:label "parts per notation unit") +SubClassOf( ) + +# Class: (parts per hundred) + +AnnotationAssertion(rdfs:label "parts per hundred") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per thousand) + +AnnotationAssertion(rdfs:label "parts per thousand") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per million) + +AnnotationAssertion(rdfs:label "parts per million") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per billion) + +AnnotationAssertion(rdfs:label "parts per billion") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per trillion) + +AnnotationAssertion(rdfs:label "parts per trillion") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (parts per quadrillion) + +AnnotationAssertion(rdfs:label "parts per quadrillion") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gram per milliliter) + +AnnotationAssertion(rdfs:label "gram per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilogram per liter) + +AnnotationAssertion(rdfs:label "kilogram per liter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gram per liter) + +AnnotationAssertion( "g per L") +AnnotationAssertion( "g/L") +AnnotationAssertion(rdfs:label "gram per liter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligram per milliliter) + +AnnotationAssertion( "mg per ml") +AnnotationAssertion( "mg/ml") +AnnotationAssertion(rdfs:label "milligram per milliliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (unit per volume unit) + +AnnotationAssertion(rdfs:label "unit per volume unit") +SubClassOf( ) + +# Class: (unit per milliliter) + +AnnotationAssertion(rdfs:label "unit per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (unit per liter) + +AnnotationAssertion(rdfs:label "unit per liter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mass per unit volume) + +AnnotationAssertion(rdfs:label "mass per unit volume") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (enzyme unit) + +AnnotationAssertion(rdfs:label "enzyme unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (density unit) + +AnnotationAssertion(rdfs:label "density unit") +SubClassOf( ) + +# Class: (linear density unit) + +AnnotationAssertion(rdfs:label "linear density unit") +SubClassOf( ) + +# Class: (kilogram per meter) + +AnnotationAssertion(rdfs:label "kilogram per meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (degree) + +AnnotationAssertion(rdfs:label "degree") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (dimensionless unit) + +AnnotationAssertion(rdfs:label "dimensionless unit") +SubClassOf( ) + +# Class: (percent) + +AnnotationAssertion(rdfs:label "percent") +SubClassOf( ) + +# Class: (pi) + +AnnotationAssertion(rdfs:label "pi") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (count unit) + +AnnotationAssertion(rdfs:label "count unit") +SubClassOf( ) + +# Class: (ratio unit) + +AnnotationAssertion(rdfs:label "ratio unit") +SubClassOf( ) + +# Class: (fraction) + +AnnotationAssertion(rdfs:label "fraction") +SubClassOf( ) + +# Class: (molecule count) + +AnnotationAssertion(rdfs:label "molecule count") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (purity percentage) + +AnnotationAssertion(rdfs:label "purity percentage") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (confluence percentage) + +AnnotationAssertion(rdfs:label "confluence percentage") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (degree Fahrenheit) + +AnnotationAssertion(rdfs:label "degree Fahrenheit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pH) + +AnnotationAssertion(rdfs:label "pH") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (liter per kilogram) + +AnnotationAssertion(rdfs:label "liter per kilogram") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milliliter per kilogram) + +AnnotationAssertion(rdfs:label "milliliter per kilogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microliter per kilogram) + +AnnotationAssertion(rdfs:label "microliter per kilogram") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell concentration unit) + +AnnotationAssertion(rdfs:label "cell concentration unit") +SubClassOf( ) + +# Class: (cells per milliliter) + +AnnotationAssertion(rdfs:label "cells per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (catalytic (activity) concentration unit) + +AnnotationAssertion(rdfs:label "catalytic (activity) concentration unit") +SubClassOf( ) + +# Class: (katal per cubic meter) + +AnnotationAssertion(rdfs:label "katal per cubic meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (katal per liter) + +AnnotationAssertion(rdfs:label "katal per liter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (volume per unit volume) + +AnnotationAssertion(rdfs:label "volume per unit volume") +SubClassOf( ) + +# Class: (milliliter per cubic meter) + +AnnotationAssertion(rdfs:label "milliliter per cubic meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milliliter per liter) + +AnnotationAssertion( "ml per L") +AnnotationAssertion( "ml/l") +AnnotationAssertion(rdfs:label "milliliter per liter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gram per deciliter) + +AnnotationAssertion( "g/dl") +AnnotationAssertion(rdfs:label "gram per deciliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (deciliter) + +AnnotationAssertion(rdfs:label "deciliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (colony forming unit) + +AnnotationAssertion(rdfs:label "colony forming unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (plaque forming unit) + +AnnotationAssertion(rdfs:label "plaque forming unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (colony forming unit per volume) + +AnnotationAssertion(rdfs:label "colony forming unit per volume") +SubClassOf( ) + +# Class: (colony forming unit per milliliter) + +AnnotationAssertion(rdfs:label "colony forming unit per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (plaque forming unit per volume) + +AnnotationAssertion(rdfs:label "plaque forming unit per volume") +SubClassOf( ) + +# Class: (plaque forming unit per milliliter) + +AnnotationAssertion(rdfs:label "plaque forming unit per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (disintegrations per second) + +AnnotationAssertion(rdfs:label "disintegrations per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (electric potential difference unit) + +AnnotationAssertion(rdfs:label "electric potential difference unit") +SubClassOf( ) + +# Class: (volt) + +AnnotationAssertion(rdfs:label "volt") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (electric charge) + +AnnotationAssertion(rdfs:label "electric charge") +SubClassOf( ) + +# Class: (coulomb) + +AnnotationAssertion(rdfs:label "coulomb") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (dalton) + +AnnotationAssertion(rdfs:label "dalton") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilodalton) + +AnnotationAssertion(rdfs:label "kilodalton") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (watt-hour) + +AnnotationAssertion(rdfs:label "watt-hour") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilowatt-hour) + +AnnotationAssertion(rdfs:label "kilowatt-hour") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (magnetic flux unit) + +AnnotationAssertion(rdfs:label "magnetic flux unit") +SubClassOf( ) + +# Class: (weber) + +AnnotationAssertion(rdfs:label "weber") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (magnetic flux density unit) + +AnnotationAssertion(rdfs:label "magnetic flux density unit") +SubClassOf( ) + +# Class: (tesla) + +AnnotationAssertion(rdfs:label "tesla") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (volt-hour) + +AnnotationAssertion(rdfs:label "volt-hour") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilovolt-hour) + +AnnotationAssertion(rdfs:label "kilovolt-hour") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (information unit) + +AnnotationAssertion(rdfs:label "information unit") +SubClassOf( ) + +# Class: (bit) + +AnnotationAssertion(rdfs:label "bit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (byte) + +AnnotationAssertion(rdfs:label "byte") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilobyte) + +AnnotationAssertion(rdfs:label "kilobyte") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (megabyte) + +AnnotationAssertion(rdfs:label "megabyte") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (image resolution unit) + +AnnotationAssertion(rdfs:label "image resolution unit") +SubClassOf( ) + +# Class: (chroma sampling unit) + +AnnotationAssertion(rdfs:label "chroma sampling unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (dynamic range unit) + +AnnotationAssertion(rdfs:label "dynamic range unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (spatial resolution unit) + +AnnotationAssertion(rdfs:label "spatial resolution unit") +SubClassOf( ) + +# Class: (dots per inch) + +AnnotationAssertion(rdfs:label "dots per inch") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (micron pixel) + +AnnotationAssertion(rdfs:label "micron pixel") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pixels per inch) + +AnnotationAssertion(rdfs:label "pixels per inch") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pixels per millimeter) + +AnnotationAssertion(rdfs:label "pixels per millimeter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (base pair) + +AnnotationAssertion(rdfs:label "base pair") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kibibyte) + +AnnotationAssertion(rdfs:label "kibibyte") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mebibyte) + +AnnotationAssertion(rdfs:label "mebibyte") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millivolt) + +AnnotationAssertion(rdfs:label "millivolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (kilovolt) + +AnnotationAssertion(rdfs:label "kilovolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microvolt) + +AnnotationAssertion(rdfs:label "microvolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanovolt) + +AnnotationAssertion(rdfs:label "nanovolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (picovolt) + +AnnotationAssertion(rdfs:label "picovolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (megavolt) + +AnnotationAssertion(rdfs:label "megavolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (surface tension unit) + +AnnotationAssertion(rdfs:label "surface tension unit") +SubClassOf( ) + +# Class: (newton per meter) + +AnnotationAssertion(rdfs:label "newton per meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (dyne per cm) + +AnnotationAssertion(rdfs:label "dyne per cm") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (viscosity unit) + +AnnotationAssertion(rdfs:label "viscosity unit") +SubClassOf( ) + +# Class: (pascal second) + +AnnotationAssertion(rdfs:label "pascal second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (poise) + +AnnotationAssertion(rdfs:label "poise") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (decibel) + +AnnotationAssertion(rdfs:label "decibel") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (effective dose unit) + +AnnotationAssertion(rdfs:label "effective dose unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (conduction unit) + +AnnotationAssertion(rdfs:label "conduction unit") +SubClassOf( ) + +# Class: (electrical conduction unit) + +AnnotationAssertion(rdfs:label "electrical conduction unit") +SubClassOf( ) + +# Class: (heat conduction unit) + +AnnotationAssertion(rdfs:label "heat conduction unit") +SubClassOf( ) + +# Class: (siemens) + +AnnotationAssertion(rdfs:label "siemens") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (watt per meter kelvin) + +AnnotationAssertion(rdfs:label "watt per meter kelvin") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (electronvolt) + +AnnotationAssertion(rdfs:label "electronvolt") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (electric field strength unit) + +AnnotationAssertion(rdfs:label "electric field strength unit") +SubClassOf( ) + +# Class: (volt per meter) + +AnnotationAssertion(rdfs:label "volt per meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (absorbance unit) + +AnnotationAssertion(rdfs:label "absorbance unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (volumetric flow rate unit) + +AnnotationAssertion(rdfs:label "volumetric flow rate unit") +SubClassOf( ) + +# Class: (microliters per minute) + +AnnotationAssertion(rdfs:label "microliters per minute") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millimetres of mercury) + +AnnotationAssertion(rdfs:label "millimetres of mercury") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligram per liter) + +AnnotationAssertion(rdfs:label "milligram per liter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microgram per milliliter) + +AnnotationAssertion(rdfs:label "microgram per milliliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nanogram per milliliter) + +AnnotationAssertion(rdfs:label "nanogram per milliliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (milliunits per milliliter) + +AnnotationAssertion(rdfs:label "milliunits per milliliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (rate unit) + +AnnotationAssertion(rdfs:label "rate unit") +SubClassOf( ) + +# Class: (count per nanomolar second) + +AnnotationAssertion(rdfs:label "count per nanomolar second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (count per molar second) + +AnnotationAssertion(rdfs:label "count per molar second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilogram per hectare) + +AnnotationAssertion(rdfs:label "kilogram per hectare") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (count per nanomolar) + +AnnotationAssertion(rdfs:label "count per nanomolar") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (count per molar) + +AnnotationAssertion(rdfs:label "count per molar") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (giga) + +AnnotationAssertion(rdfs:label "giga") +SubClassOf( ) + +# Class: (mega) + +AnnotationAssertion(rdfs:label "mega") +SubClassOf( ) + +# Class: (kilo) + +AnnotationAssertion(rdfs:label "kilo") +SubClassOf( ) + +# Class: (deci) + +AnnotationAssertion(rdfs:label "deci") +SubClassOf( ) + +# Class: (milli) + +AnnotationAssertion(rdfs:label "milli") +SubClassOf( ) + +# Class: (centi) + +AnnotationAssertion(rdfs:label "centi") +SubClassOf( ) + +# Class: (micro) + +AnnotationAssertion(rdfs:label "micro") +SubClassOf( ) + +# Class: (nano) + +AnnotationAssertion(rdfs:label "nano") +SubClassOf( ) + +# Class: (microgram per liter) + +AnnotationAssertion( "ng/ml") +AnnotationAssertion( "ug/L") +AnnotationAssertion(rdfs:label "microgram per liter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pico) + +AnnotationAssertion(rdfs:label "pico") +SubClassOf( ) + +# Class: (femto) + +AnnotationAssertion(rdfs:label "femto") +SubClassOf( ) + +# Class: (atto) + +AnnotationAssertion(rdfs:label "atto") +SubClassOf( ) + +# Class: (dose unit) + +AnnotationAssertion(rdfs:label "dose unit") +SubClassOf( ) + +# Class: (milligram per kilogram) + +AnnotationAssertion(rdfs:label "milligram per kilogram") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligram per square meter) + +AnnotationAssertion(rdfs:label "milligram per square meter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (dosage unit) + +AnnotationAssertion(rdfs:label "dosage unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligram per kilogram per day) + +AnnotationAssertion(rdfs:label "milligram per kilogram per day") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (relative light unit) + +AnnotationAssertion(rdfs:label "relative light unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (relative luminescence unit) + +AnnotationAssertion(rdfs:label "relative luminescence unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (relative fluorescence unit) + +AnnotationAssertion(rdfs:label "relative fluorescence unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (megaHertz) + +AnnotationAssertion(rdfs:label "megaHertz") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (centiMorgan) + +AnnotationAssertion(rdfs:label "centiMorgan") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (centiRay) + +AnnotationAssertion(rdfs:label "centiRay") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (mega base pair) + +AnnotationAssertion(rdfs:label "mega base pair") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (giga base pair) + +AnnotationAssertion(rdfs:label "giga base pair") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (square micrometer) + +AnnotationAssertion(rdfs:label "square micrometer") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millisiemens) + +AnnotationAssertion(rdfs:label "millisiemens") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (micromole per litre) + +AnnotationAssertion(rdfs:label "micromole per litre") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (micromole per kilogram) + +AnnotationAssertion(rdfs:label "micromole per kilogram") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (millimeters per day) + +AnnotationAssertion(rdfs:label "millimeters per day") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilometer per hour) + +AnnotationAssertion(rdfs:label "kilometer per hour") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milli) + +AnnotationAssertion(rdfs:label "milli") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (hectare) + +AnnotationAssertion(rdfs:label "hectare") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (inch) + +AnnotationAssertion(rdfs:label "inch") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (thou) + +AnnotationAssertion(rdfs:label "thou") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (foot) + +AnnotationAssertion(rdfs:label "foot") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (yard) + +AnnotationAssertion(rdfs:label "yard") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (chain) + +AnnotationAssertion(rdfs:label "chain") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (furlong) + +AnnotationAssertion(rdfs:label "furlong") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (mile) + +AnnotationAssertion(rdfs:label "mile") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (league) + +AnnotationAssertion(rdfs:label "league") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ) + +# Class: (maritime length unit) + +AnnotationAssertion(rdfs:label "maritime length unit") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (fathom) + +AnnotationAssertion(rdfs:label "fathom") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (cable) + +AnnotationAssertion(rdfs:label "cable") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (nautical mile) + +AnnotationAssertion(rdfs:label "nautical mile") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (perch) + +AnnotationAssertion(rdfs:label "perch") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (rood) + +AnnotationAssertion(rdfs:label "rood") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (acre) + +AnnotationAssertion(rdfs:label "acre") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (fluid ounce) + +AnnotationAssertion(rdfs:label "fluid ounce") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gill) + +AnnotationAssertion(rdfs:label "gill") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pint) + +AnnotationAssertion(rdfs:label "pint") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (quart) + +AnnotationAssertion(rdfs:label "quart") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gallon) + +AnnotationAssertion(rdfs:label "gallon") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (grain) + +AnnotationAssertion(rdfs:label "grain") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (drachm) + +AnnotationAssertion(rdfs:label "drachm") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (ounce) + +AnnotationAssertion(rdfs:label "ounce") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (pound) + +AnnotationAssertion(rdfs:label "pound") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (stone) + +AnnotationAssertion(rdfs:label "stone") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (quarter) + +AnnotationAssertion(rdfs:label "quarter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (hundredweight) + +AnnotationAssertion(rdfs:label "hundredweight") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (ton) + +AnnotationAssertion(rdfs:label "ton") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (slug) + +AnnotationAssertion(rdfs:label "slug") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (teaspoon) + +AnnotationAssertion(rdfs:label "teaspoon") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (micromole) + +AnnotationAssertion(rdfs:label "micromole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gram per square meter) + +AnnotationAssertion(rdfs:label "gram per square meter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (nanogram per microliter) + +AnnotationAssertion(rdfs:label "nanogram per microliter") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (large calorie) + +AnnotationAssertion(rdfs:label "large calorie") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (micrograms per wheaton bottle) + +AnnotationAssertion(rdfs:label "micrograms per wheaton bottle") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (picoampere) + +AnnotationAssertion(rdfs:label "picoampere") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (centigray) + +AnnotationAssertion(rdfs:label "centigray") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gigaelectronvolt) + +AnnotationAssertion(rdfs:label "gigaelectronvolt") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gigaelectronvolt per nucleon) + +AnnotationAssertion(rdfs:label "gigaelectronvolt per nucleon") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (megaelectronvolt per nucleon) + +AnnotationAssertion(rdfs:label "megaelectronvolt per nucleon") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kiloelectronvolt per micron) + +AnnotationAssertion(rdfs:label "kiloelectronvolt per micron") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (gray per minute) + +AnnotationAssertion(rdfs:label "gray per minute") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (centigray per minute) + +AnnotationAssertion(rdfs:label "centigray per minute") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (milligray per minute) + +AnnotationAssertion(rdfs:label "milligray per minute") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (milligray per day) + +AnnotationAssertion(rdfs:label "milligray per day") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligray per hour) + +AnnotationAssertion(rdfs:label "milligray per hour") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (milligray per second) + +AnnotationAssertion(rdfs:label "milligray per second") +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) + +# Class: (kilometer) + +AnnotationAssertion(rdfs:label "kilometer") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (milligram per deciliter) + +AnnotationAssertion(rdfs:label "milligram per deciliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (microgram per deciliter) + +AnnotationAssertion(rdfs:label "microgram per deciliter") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectOneOf()) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (meter based unit) + +AnnotationAssertion(rdfs:label "meter based unit") +SubClassOf( ) + +# Class: (second based unit) + +AnnotationAssertion(rdfs:label "second based unit") +SubClassOf( ) + +# Class: (ampere based unit) + +AnnotationAssertion(rdfs:label "ampere based unit") +SubClassOf( ) + +# Class: (kelvin based unit) + +AnnotationAssertion(rdfs:label "kelvin based unit") +SubClassOf( ) + +# Class: (mole based unit) + +AnnotationAssertion(rdfs:label "mole based unit") +SubClassOf( ) + +# Class: (candela based unit) + +AnnotationAssertion(rdfs:label "candela based unit") +SubClassOf( ) + +# Class: (angstrom based unit) + +AnnotationAssertion(rdfs:label "angstrom based unit") +SubClassOf( ) + +# Class: (gram based unit) + +AnnotationAssertion(rdfs:label "gram based unit") +SubClassOf( ) + +# Class: (degree Celsius based unit) + +AnnotationAssertion(rdfs:label "degree Celsius based unit") +SubClassOf( ) + +# Class: (minute based unit) + +AnnotationAssertion(rdfs:label "minute based unit") +SubClassOf( ) + +# Class: (hour based unit) + +AnnotationAssertion(rdfs:label "hour based unit") +SubClassOf( ) + +# Class: (day based unit) + +AnnotationAssertion(rdfs:label "day based unit") +SubClassOf( ) + +# Class: (week based unit) + +AnnotationAssertion(rdfs:label "week based unit") +SubClassOf( ) + +# Class: (month based unit) + +AnnotationAssertion(rdfs:label "month based unit") +SubClassOf( ) + +# Class: (year based unit) + +AnnotationAssertion(rdfs:label "year based unit") +SubClassOf( ) + +# Class: (molar based unit) + +AnnotationAssertion(rdfs:label "molar based unit") +SubClassOf( ) + +# Class: (molal based unit) + +AnnotationAssertion(rdfs:label "molal based unit") +SubClassOf( ) + +# Class: (normal based unit) + +AnnotationAssertion(rdfs:label "normal based unit") +SubClassOf( ) + +# Class: (mole fraction based unit) + +AnnotationAssertion(rdfs:label "mole fraction based unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (meter per second per second based unit) + +AnnotationAssertion(rdfs:label "meter per second per second based unit") +SubClassOf( ) + +# Class: (radian per second per second based unit) + +AnnotationAssertion(rdfs:label "radian per second per second based unit") +SubClassOf( ) + +# Class: (radian per second based unit) + +AnnotationAssertion(rdfs:label "radian per second based unit") +SubClassOf( ) + +# Class: (square meter based unit) + +AnnotationAssertion(rdfs:label "square meter based unit") +SubClassOf( ) + +# Class: (square centimeter based unit) + +AnnotationAssertion(rdfs:label "square centimeter based unit") +SubClassOf( ) + +# Class: (square millimeter based unit) + +AnnotationAssertion(rdfs:label "square millimeter based unit") +SubClassOf( ) + +# Class: (gram per cubic centimeter based unit) + +AnnotationAssertion(rdfs:label "gram per cubic centimeter based unit") +SubClassOf( ) + +# Class: (candela per square meter based unit) + +AnnotationAssertion(rdfs:label "candela per square meter based unit") +SubClassOf( ) + +# Class: (gram per mole based unit) + +AnnotationAssertion(rdfs:label "gram per mole based unit") +SubClassOf( ) + +# Class: (cubic meter per mole based unit) + +AnnotationAssertion(rdfs:label "cubic meter per mole based unit") +SubClassOf( ) + +# Class: (cubic centimeter per mole based unit) + +AnnotationAssertion(rdfs:label "cubic centimeter per mole based unit") +SubClassOf( ) + +# Class: (turns per second based unit) + +AnnotationAssertion(rdfs:label "turns per second based unit") +SubClassOf( ) + +# Class: (cubic meter per kilogram based unit) + +AnnotationAssertion(rdfs:label "cubic meter per kilogram based unit") +SubClassOf( ) + +# Class: (meter per second based unit) + +AnnotationAssertion(rdfs:label "meter per second based unit") +SubClassOf( ) + +# Class: (cubic meter based unit) + +AnnotationAssertion(rdfs:label "cubic meter based unit") +SubClassOf( ) + +# Class: (cubic centimeter based unit) + +AnnotationAssertion(rdfs:label "cubic centimeter based unit") +SubClassOf( ) + +# Class: (liter based unit) + +AnnotationAssertion(rdfs:label "liter based unit") +SubClassOf( ) + +# Class: (cubic decimeter based unit) + +AnnotationAssertion(rdfs:label "cubic decimeter based unit") +SubClassOf( ) + +# Class: (hertz based unit) + +AnnotationAssertion(rdfs:label "hertz based unit") +SubClassOf( ) + +# Class: (newton based unit) + +AnnotationAssertion(rdfs:label "newton based unit") +SubClassOf( ) + +# Class: (pascal based unit) + +AnnotationAssertion(rdfs:label "pascal based unit") +SubClassOf( ) + +# Class: (joule based unit) + +AnnotationAssertion(rdfs:label "joule based unit") +SubClassOf( ) + +# Class: (watt based unit) + +AnnotationAssertion(rdfs:label "watt based unit") +SubClassOf( ) + +# Class: (lux based unit) + +AnnotationAssertion(rdfs:label "lux based unit") +SubClassOf( ) + +# Class: (lumen based unit) + +AnnotationAssertion(rdfs:label "lumen based unit") +SubClassOf( ) + +# Class: (katal based unit) + +AnnotationAssertion(rdfs:label "katal based unit") +SubClassOf( ) + +# Class: (radian based unit) + +AnnotationAssertion(rdfs:label "radian based unit") +SubClassOf( ) + +# Class: (steradian based unit) + +AnnotationAssertion(rdfs:label "steradian based unit") +SubClassOf( ) + +# Class: (becquerel based unit) + +AnnotationAssertion(rdfs:label "becquerel based unit") +SubClassOf( ) + +# Class: (curie based unit) + +AnnotationAssertion(rdfs:label "curie based unit") +SubClassOf( ) + +# Class: (gray based unit) + +AnnotationAssertion(rdfs:label "gray based unit") +SubClassOf( ) + +# Class: (rad based unit) + +AnnotationAssertion(rdfs:label "rad based unit") +SubClassOf( ) + +# Class: (roentgen based unit) + +AnnotationAssertion(rdfs:label "roentgen based unit") +SubClassOf( ) + +# Class: (sievert based unit) + +AnnotationAssertion(rdfs:label "sievert based unit") +SubClassOf( ) + +# Class: (Roentgen equivalent man based unit) + +AnnotationAssertion(rdfs:label "Roentgen equivalent man based unit") +SubClassOf( ) + +# Class: (disintegrations per minute based unit) + +AnnotationAssertion(rdfs:label "disintegrations per minute based unit") +SubClassOf( ) + +# Class: (counts per minute based unit) + +AnnotationAssertion(rdfs:label "counts per minute based unit") +SubClassOf( ) + +# Class: (century based unit) + +AnnotationAssertion(rdfs:label "century based unit") +SubClassOf( ) + +# Class: (half life based unit) + +AnnotationAssertion(rdfs:label "half life based unit") +SubClassOf( ) + +# Class: (foot candle based unit) + +AnnotationAssertion(rdfs:label "foot candle based unit") +SubClassOf( ) + +# Class: (watt per square meter based unit) + +AnnotationAssertion(rdfs:label "watt per square meter based unit") +SubClassOf( ) + +# Class: (einstein per square meter per second based unit) + +AnnotationAssertion(rdfs:label "einstein per square meter per second based unit") +SubClassOf( ) + +# Class: (watt per steradian per square meter based unit) + +AnnotationAssertion(rdfs:label "watt per steradian per square meter based unit") +SubClassOf( ) + +# Class: (watt per steradian based unit) + +AnnotationAssertion(rdfs:label "watt per steradian based unit") +SubClassOf( ) + +# Class: (mass percentage based unit) + +AnnotationAssertion(rdfs:label "mass percentage based unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (mass volume percentage based unit) + +AnnotationAssertion(rdfs:label "mass volume percentage based unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (volume percentage based unit) + +AnnotationAssertion(rdfs:label "volume percentage based unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (parts per hundred based unit) + +AnnotationAssertion(rdfs:label "parts per hundred based unit") +SubClassOf( ) + +# Class: (parts per thousand based unit) + +AnnotationAssertion(rdfs:label "parts per thousand based unit") +SubClassOf( ) + +# Class: (parts per million based unit) + +AnnotationAssertion(rdfs:label "parts per million based unit") +SubClassOf( ) + +# Class: (parts per billion based unit) + +AnnotationAssertion(rdfs:label "parts per billion based unit") +SubClassOf( ) + +# Class: (parts per trillion based unit) + +AnnotationAssertion(rdfs:label "parts per trillion based unit") +SubClassOf( ) + +# Class: (parts per quadrillion based unit) + +AnnotationAssertion(rdfs:label "parts per quadrillion based unit") +SubClassOf( ) + +# Class: (gram per milliliter based unit) + +AnnotationAssertion(rdfs:label "gram per milliliter based unit") +SubClassOf( ) + +# Class: (gram per liter based unit) + +AnnotationAssertion(rdfs:label "gram per liter based unit") +SubClassOf( ) + +# Class: (unit per milliliter based unit) + +AnnotationAssertion(rdfs:label "unit per milliliter based unit") +SubClassOf( ) + +# Class: (unit per liter based unit) + +AnnotationAssertion(rdfs:label "unit per liter based unit") +SubClassOf( ) + +# Class: (mass per unit volume based unit) + +AnnotationAssertion(rdfs:label "mass per unit volume based unit") +SubClassOf( ) + +# Class: (enzyme unit based unit) + +AnnotationAssertion(rdfs:label "enzyme unit based unit") +SubClassOf( ) + +# Class: (degree based unit) + +AnnotationAssertion(rdfs:label "degree based unit") +SubClassOf( ) + +# Class: (pi based unit) + +AnnotationAssertion(rdfs:label "pi based unit") +SubClassOf( ) + +# Class: (molecule count based unit) + +AnnotationAssertion(rdfs:label "molecule count based unit") +SubClassOf( ) + +# Class: (purity percentage based unit) + +AnnotationAssertion(rdfs:label "purity percentage based unit") +SubClassOf( ) + +# Class: (confluence percentage based unit) + +AnnotationAssertion(rdfs:label "confluence percentage based unit") +SubClassOf( ) + +# Class: (degree Fahrenheit based unit) + +AnnotationAssertion(rdfs:label "degree Fahrenheit based unit") +SubClassOf( ) + +# Class: (pH based unit) + +AnnotationAssertion(rdfs:label "pH based unit") +SubClassOf( ) +SubClassOf( ) + +# Class: (liter per kilogram based unit) + +AnnotationAssertion(rdfs:label "liter per kilogram based unit") +SubClassOf( ) + +# Class: (cells per milliliter based unit) + +AnnotationAssertion(rdfs:label "cells per milliliter based unit") +SubClassOf( ) + +# Class: (katal per cubic meter based unit) + +AnnotationAssertion(rdfs:label "katal per cubic meter based unit") +SubClassOf( ) + +# Class: (katal per liter based unit) + +AnnotationAssertion(rdfs:label "katal per liter based unit") +SubClassOf( ) + +# Class: (gram per deciliter based unit) + +AnnotationAssertion(rdfs:label "gram per deciliter based unit") +SubClassOf( ) + +# Class: (colony forming unit based unit) + +AnnotationAssertion(rdfs:label "colony forming unit based unit") +SubClassOf( ) + +# Class: (plaque forming unit based unit) + +AnnotationAssertion(rdfs:label "plaque forming unit based unit") +SubClassOf( ) + +# Class: (colony forming unit per milliliter based unit) + +AnnotationAssertion(rdfs:label "colony forming unit per milliliter based unit") +SubClassOf( ) + +# Class: (plaque forming unit per milliliter based unit) + +AnnotationAssertion(rdfs:label "plaque forming unit per milliliter based unit") +SubClassOf( ) + +# Class: (disintegrations per second based unit) + +AnnotationAssertion(rdfs:label "disintegrations per second based unit") +SubClassOf( ) + +# Class: (volt based unit) + +AnnotationAssertion(rdfs:label "volt based unit") +SubClassOf( ) + +# Class: (coulomb based unit) + +AnnotationAssertion(rdfs:label "coulomb based unit") +SubClassOf( ) + +# Class: (dalton based unit) + +AnnotationAssertion(rdfs:label "dalton based unit") +SubClassOf( ) + +# Class: (watt-hour based unit) + +AnnotationAssertion(rdfs:label "watt-hour based unit") +SubClassOf( ) + +# Class: (weber based unit) + +AnnotationAssertion(rdfs:label "weber based unit") +SubClassOf( ) + +# Class: (tesla based unit) + +AnnotationAssertion(rdfs:label "tesla based unit") +SubClassOf( ) + +# Class: (volt-hour based unit) + +AnnotationAssertion(rdfs:label "volt-hour based unit") +SubClassOf( ) + +# Class: (bit based unit) + +AnnotationAssertion(rdfs:label "bit based unit") +SubClassOf( ) + +# Class: (byte based unit) + +AnnotationAssertion(rdfs:label "byte based unit") +SubClassOf( ) + +# Class: (chroma sampling unit based unit) + +AnnotationAssertion(rdfs:label "chroma sampling unit based unit") +SubClassOf( ) + +# Class: (dynamic range unit based unit) + +AnnotationAssertion(rdfs:label "dynamic range unit based unit") +SubClassOf( ) + +# Class: (dots per inch based unit) + +AnnotationAssertion(rdfs:label "dots per inch based unit") +SubClassOf( ) + +# Class: (pixels per inch based unit) + +AnnotationAssertion(rdfs:label "pixels per inch based unit") +SubClassOf( ) + +# Class: (pixels per millimeter based unit) + +AnnotationAssertion(rdfs:label "pixels per millimeter based unit") +SubClassOf( ) + +# Class: (base pair based unit) + +AnnotationAssertion(rdfs:label "base pair based unit") +SubClassOf( ) + +# Class: (kibibyte based unit) + +AnnotationAssertion(rdfs:label "kibibyte based unit") +SubClassOf( ) + +# Class: (mebibyte based unit) + +AnnotationAssertion(rdfs:label "mebibyte based unit") +SubClassOf( ) + +# Class: (newton per meter based unit) + +AnnotationAssertion(rdfs:label "newton per meter based unit") +SubClassOf( ) + +# Class: (dyne per cm based unit) + +AnnotationAssertion(rdfs:label "dyne per cm based unit") +SubClassOf( ) + +# Class: (pascal second based unit) + +AnnotationAssertion(rdfs:label "pascal second based unit") +SubClassOf( ) + +# Class: (poise based unit) + +AnnotationAssertion(rdfs:label "poise based unit") +SubClassOf( ) + +# Class: (effective dose unit based unit) + +AnnotationAssertion(rdfs:label "effective dose unit based unit") +SubClassOf( ) + +# Class: (siemens based unit) + +AnnotationAssertion(rdfs:label "siemens based unit") +SubClassOf( ) + +# Class: (watt per meter kelvin based unit) + +AnnotationAssertion(rdfs:label "watt per meter kelvin based unit") +SubClassOf( ) + +# Class: (electronvolt based unit) + +AnnotationAssertion(rdfs:label "electronvolt based unit") +SubClassOf( ) + +# Class: (volt per meter based unit) + +AnnotationAssertion(rdfs:label "volt per meter based unit") +SubClassOf( ) + +# Class: (absorbance unit based unit) + +AnnotationAssertion(rdfs:label "absorbance unit based unit") +SubClassOf( ) + +# Class: (count per nanomolar second based unit) + +AnnotationAssertion(rdfs:label "count per nanomolar second based unit") +SubClassOf( ) + +# Class: (count per molar second based unit) + +AnnotationAssertion(rdfs:label "count per molar second based unit") +SubClassOf( ) + +# Class: (count per nanomolar based unit) + +AnnotationAssertion(rdfs:label "count per nanomolar based unit") +SubClassOf( ) + +# Class: (count per molar based unit) + +AnnotationAssertion(rdfs:label "count per molar based unit") +SubClassOf( ) + +# Class: (dosage unit based unit) + +AnnotationAssertion(rdfs:label "dosage unit based unit") +SubClassOf( ) + +# Class: (relative light unit based unit) + +AnnotationAssertion(rdfs:label "relative light unit based unit") +SubClassOf( ) + +# Class: (relative luminescence unit based unit) + +AnnotationAssertion(rdfs:label "relative luminescence unit based unit") +SubClassOf( ) + +# Class: (relative fluorescence unit based unit) + +AnnotationAssertion(rdfs:label "relative fluorescence unit based unit") +SubClassOf( ) + +# Class: (square micrometer based unit) + +AnnotationAssertion(rdfs:label "square micrometer based unit") +SubClassOf( ) + +# Class: (hectare based unit) + +AnnotationAssertion(rdfs:label "hectare based unit") +SubClassOf( ) + +# Class: (inch based unit) + +AnnotationAssertion(rdfs:label "inch based unit") +SubClassOf( ) + +# Class: (thou based unit) + +AnnotationAssertion(rdfs:label "thou based unit") +SubClassOf( ) + +# Class: (foot based unit) + +AnnotationAssertion(rdfs:label "foot based unit") +SubClassOf( ) + +# Class: (yard based unit) + +AnnotationAssertion(rdfs:label "yard based unit") +SubClassOf( ) + +# Class: (chain based unit) + +AnnotationAssertion(rdfs:label "chain based unit") +SubClassOf( ) + +# Class: (furlong based unit) + +AnnotationAssertion(rdfs:label "furlong based unit") +SubClassOf( ) + +# Class: (mile based unit) + +AnnotationAssertion(rdfs:label "mile based unit") +SubClassOf( ) + +# Class: (league based unit) + +AnnotationAssertion(rdfs:label "league based unit") +SubClassOf( ) + +# Class: (maritime length unit based unit) + +AnnotationAssertion(rdfs:label "maritime length unit based unit") +SubClassOf( ) + +# Class: (fathom based unit) + +AnnotationAssertion(rdfs:label "fathom based unit") +SubClassOf( ) + +# Class: (cable based unit) + +AnnotationAssertion(rdfs:label "cable based unit") +SubClassOf( ) + +# Class: (nautical mile based unit) + +AnnotationAssertion(rdfs:label "nautical mile based unit") +SubClassOf( ) + +# Class: (perch based unit) + +AnnotationAssertion(rdfs:label "perch based unit") +SubClassOf( ) + +# Class: (rood based unit) + +AnnotationAssertion(rdfs:label "rood based unit") +SubClassOf( ) + +# Class: (acre based unit) + +AnnotationAssertion(rdfs:label "acre based unit") +SubClassOf( ) + +# Class: (fluid ounce based unit) + +AnnotationAssertion(rdfs:label "fluid ounce based unit") +SubClassOf( ) + +# Class: (gill based unit) + +AnnotationAssertion(rdfs:label "gill based unit") +SubClassOf( ) + +# Class: (pint based unit) + +AnnotationAssertion(rdfs:label "pint based unit") +SubClassOf( ) + +# Class: (quart based unit) + +AnnotationAssertion(rdfs:label "quart based unit") +SubClassOf( ) + +# Class: (gallon based unit) + +AnnotationAssertion(rdfs:label "gallon based unit") +SubClassOf( ) + +# Class: (grain based unit) + +AnnotationAssertion(rdfs:label "grain based unit") +SubClassOf( ) + +# Class: (drachm based unit) + +AnnotationAssertion(rdfs:label "drachm based unit") +SubClassOf( ) + +# Class: (ounce based unit) + +AnnotationAssertion(rdfs:label "ounce based unit") +SubClassOf( ) + +# Class: (pound based unit) + +AnnotationAssertion(rdfs:label "pound based unit") +SubClassOf( ) + +# Class: (stone based unit) + +AnnotationAssertion(rdfs:label "stone based unit") +SubClassOf( ) + +# Class: (quarter based unit) + +AnnotationAssertion(rdfs:label "quarter based unit") +SubClassOf( ) + +# Class: (hundredweight based unit) + +AnnotationAssertion(rdfs:label "hundredweight based unit") +SubClassOf( ) + +# Class: (ton based unit) + +AnnotationAssertion(rdfs:label "ton based unit") +SubClassOf( ) + +# Class: (slug based unit) + +AnnotationAssertion(rdfs:label "slug based unit") +SubClassOf( ) + +# Class: (teaspoon based unit) + +AnnotationAssertion(rdfs:label "teaspoon based unit") +SubClassOf( ) + +# Class: (gram per square meter based unit) + +AnnotationAssertion(rdfs:label "gram per square meter based unit") +SubClassOf( ) + +# Class: (large calorie based unit) + +AnnotationAssertion(rdfs:label "large calorie based unit") +SubClassOf( ) + +# Class: (gray per minute based unit) + +AnnotationAssertion(rdfs:label "gray per minute based unit") +SubClassOf( ) + +# Class: (Obsolete Class) + +AnnotationAssertion(rdfs:label "Obsolete Class") + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg") +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (obsolete_core) + +AnnotationAssertion( "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolete_core"@en) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (obsolete_other) + +AnnotationAssertion( "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason."@en) +AnnotationAssertion( "We expect to be able to mine these new reasons and add instances as required."@en) +AnnotationAssertion(rdfs:label "obsolete_other"@en) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + +# Individual: (Transformation-ML) + +AnnotationAssertion( "Transformation-ML"@en) +AnnotationAssertion( "Transformation-ML file describing parameter transformations used in a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf") +AnnotationAssertion(rdfs:label "Transformation-ML"@en) +ClassAssertion( ) + +# Individual: (ACS) + +AnnotationAssertion( "ACS"@en) +AnnotationAssertion( "d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.isac-net.org/content/view/607/150/") +AnnotationAssertion(rdfs:label "ACS"@en) +ClassAssertion( ) + +# Individual: (XML) + +AnnotationAssertion( "XML"@en) +AnnotationAssertion( "RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document"@en) +AnnotationAssertion( ) +AnnotationAssertion( "XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/XML/") +AnnotationAssertion(rdfs:label "XML"@en) +ClassAssertion( ) + +# Individual: (RDF) + +AnnotationAssertion( "RDF"@en) +AnnotationAssertion( "A FOAF file, a SKOS file, an OWL file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/RDF/") +AnnotationAssertion(rdfs:label "RDF"@en) +ClassAssertion( ) + +# Individual: (zip) + +AnnotationAssertion( "zip"@en) +AnnotationAssertion( "MagicDraw MDZIP archive, Java JAR file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/") +AnnotationAssertion(rdfs:label "zip"@en) +ClassAssertion( ) + +# Individual: (tar) + +AnnotationAssertion( "tar"@en) +AnnotationAssertion( "Example.tar file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.gnu.org/software/tar/manual/") +AnnotationAssertion(rdfs:label "tar"@en) +ClassAssertion( ) + +# Individual: (FCS) + +AnnotationAssertion( "FCS"@en) +AnnotationAssertion( "d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.fcspress.com/") +AnnotationAssertion(rdfs:label "FCS"@en) +ClassAssertion( ) + +# Individual: (Compensation-ML) + +AnnotationAssertion( "Compensation-ML"@en) +AnnotationAssertion( "compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf") +AnnotationAssertion(rdfs:label "Compensation-ML"@en) +ClassAssertion( ) + +# Individual: (Gating-ML) + +AnnotationAssertion( "Gating-ML"@en) +AnnotationAssertion( "foogate.xml, Gating-ML file describing gates used in a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.flowcyt.org/gating/") +AnnotationAssertion(rdfs:label "Gating-ML"@en) +ClassAssertion( ) + +# Individual: (OWL) + +AnnotationAssertion( "OWL"@en) +AnnotationAssertion( "OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/2004/OWL/") +AnnotationAssertion(rdfs:label "OWL"@en) +ClassAssertion( ) + +# Individual: (Affymetrix) + +AnnotationAssertion( "Affymetrix") +AnnotationAssertion( "Affymetrix supplied microarray") +AnnotationAssertion( "An organization which supplies technology, tools and protocols for use in high throughput applications"@en) +AnnotationAssertion(rdfs:label "Affymetrix") +ClassAssertion( ) +ClassAssertion( ) + +# Individual: (Thermo) + +AnnotationAssertion( "Thermo") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Thermo") +ClassAssertion( ) + +# Individual: (Waters) + +AnnotationAssertion( "Waters") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Waters") +ClassAssertion( ) + +# Individual: (BIO-RAD) + +AnnotationAssertion( "BIO-RAD") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "BIO-RAD") +ClassAssertion( ) + +# Individual: (GenePattern hierarchical clustering) + +AnnotationAssertion( "GenePattern hierarchical clustering") +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern hierarchical clustering") +ClassAssertion( ) + +# Individual: (Ambion) + +AnnotationAssertion( "Ambion") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Ambion") +ClassAssertion( ) + +# Individual: (Helicos) + +AnnotationAssertion( "Helicos") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Helicos") +ClassAssertion( ) + +# Individual: (Roche) + +AnnotationAssertion( "Roche") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Roche") +ClassAssertion( ) + +# Individual: (Illumina) + +AnnotationAssertion( "Illumina") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Illumina") +ClassAssertion( ) + +# Individual: (GenePattern PCA) + +AnnotationAssertion( "GenePattern PCA") +AnnotationAssertion(rdfs:label "GenePattern PCA") +ClassAssertion( ) + +# Individual: (GenePattern module SVM) + +AnnotationAssertion( "GenePattern module SVM") +AnnotationAssertion( "GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion(rdfs:label "GenePattern module SVM") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern k-nearest neighbors) + +AnnotationAssertion( "GenePattern k-nearest neighbors") +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern k-nearest neighbors") +ClassAssertion( ) + +# Individual: (GenePattern LOOCV) + +AnnotationAssertion( "GenePattern LOOCV") +AnnotationAssertion(rdfs:label "GenePattern LOOCV") +ClassAssertion( ) + +# Individual: (GenePattern k-means clustering) + +AnnotationAssertion( "GenePattern k-means clustering") +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern k-means clustering") +ClassAssertion( ) + +# Individual: (Agilent) + +AnnotationAssertion( "Agilent") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Agilent") +ClassAssertion( ) + +# Individual: (GenePattern module KMeansClustering) + +AnnotationAssertion( "GenePattern module KMeansClustering") +AnnotationAssertion( "GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KMeansClustering") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern CART) + +AnnotationAssertion( "GenePattern CART") +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern CART") +ClassAssertion( ) + +# Individual: (GenePattern module CARTXValidation) + +AnnotationAssertion( "GenePattern module CARTXValidation") +AnnotationAssertion( "GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations."@en) +AnnotationAssertion(rdfs:label "GenePattern module CARTXValidation") +ClassAssertion( ) +ObjectPropertyAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (Li-Cor) + +AnnotationAssertion( "Li-Cor") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Li-Cor") +ClassAssertion( ) + +# Individual: (Bruker Corporation) + +AnnotationAssertion( "Bruker Corporation") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Bruker Corporation") +ClassAssertion( ) + +# Individual: (GenePattern module KNNXValidation) + +AnnotationAssertion( "GenePattern module KNNXValidation") +AnnotationAssertion( "GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KNNXValidation") +ClassAssertion( ) + +# Individual: (GenePattern module PeakMatch) + +AnnotationAssertion( "GenePattern module PeakMatch") +AnnotationAssertion(rdfs:label "GenePattern module PeakMatch") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module KNN) + +AnnotationAssertion( "GenePattern module KNN") +AnnotationAssertion( "GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KNN") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module HierarchicalClustering) + +AnnotationAssertion( "GenePattern module HierarchicalClustering") +AnnotationAssertion( "GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HierarchicalClustering") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern SVM) + +AnnotationAssertion( "GenePattern SVM") +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern SVM") +ClassAssertion( ) + +# Individual: (Applied Biosystems) + +AnnotationAssertion( "Applied Biosystems") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Applied Biosystems") +ClassAssertion( ) + +# Individual: (GenePattern module PCA) + +AnnotationAssertion( "GenePattern module PCA") +AnnotationAssertion( "GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module PCA") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern peak matching) + +AnnotationAssertion( "GenePattern peak matching") +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion(rdfs:label "GenePattern peak matching") +ClassAssertion( ) + +# Individual: (Bruker Daltonics) + +AnnotationAssertion( "Bruker Daltonics") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Bruker Daltonics") +ClassAssertion( ) + +# Individual: (GenePattern HeatMapViewer data visualization) + +AnnotationAssertion( "GenePattern HeatMapViewer data visualization") +AnnotationAssertion( "The GenePattern process of generating Heat Maps from clustered data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern HeatMapViewer data visualization") +ClassAssertion( ) + +# Individual: (GenePattern HierarchicalClusteringViewer data visualization) + +AnnotationAssertion( "GenePattern HierarchicalClusteringViewer data visualization") +AnnotationAssertion( "The GenePattern process of generating hierarchical clustering visualization from clustered data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern HierarchicalClusteringViewer data visualization") +ClassAssertion( ) + +# Individual: (GenePattern module HeatMapViewer) + +AnnotationAssertion( "GenePattern module HeatMapViewer") +AnnotationAssertion( "A GenePattern software module which is used to generate a heatmap view of data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HeatMapViewer") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module HierarchicalClusteringViewer) + +AnnotationAssertion( "GenePattern module HierarchicalClusteringViewer") +AnnotationAssertion( "A GenePattern software module which is used to generate a view of data that has been hierarchically clustered."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HierarchicalClusteringViewer") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (Sysmex Corporation, Kobe, Japan) + +AnnotationAssertion( "Sysmex Corporation, Kobe, Japan") +AnnotationAssertion( ) +AnnotationAssertion( "WEB:http://www.sysmex.com/@2009/08/06") +AnnotationAssertion(rdfs:label "Sysmex Corporation, Kobe, Japan") +ClassAssertion( ) + +# Individual: (U.S. Food and Drug Administration) + +AnnotationAssertion( "U.S. Food and Drug Administration") +AnnotationAssertion( "FDA") +AnnotationAssertion(rdfs:label "U.S. Food and Drug Administration") +ClassAssertion( ) + +# Individual: (right handed) + +AnnotationAssertion( "right handed") +AnnotationAssertion(rdfs:label "right handed") +ClassAssertion( ) + +# Individual: (ambidexterous) + +AnnotationAssertion( "ambidexterous") +AnnotationAssertion(rdfs:label "ambidexterous") +ClassAssertion( ) + +# Individual: (left handed) + +AnnotationAssertion( "left handed") +AnnotationAssertion(rdfs:label "left handed") +ClassAssertion( ) + +# Individual: (Edingburgh handedness inventory) + +AnnotationAssertion( "Edingburgh handedness inventory") +AnnotationAssertion( "The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg") +AnnotationAssertion( "PERSON:Jessica Turner") +AnnotationAssertion( "PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113") +AnnotationAssertion( "WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html") +AnnotationAssertion(rdfs:label "Edingburgh handedness inventory") +ClassAssertion( ) + +# Individual: (eBioscience) + +AnnotationAssertion( "eBioscience") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.ebioscience.com/@2011/04/11") +AnnotationAssertion(rdfs:label "eBioscience") +ClassAssertion( ) + +# Individual: (Cytopeia) + +AnnotationAssertion( "Cytopeia") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.cytopeia.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Cytopeia") +ClassAssertion( ) + +# Individual: (Exalpha Biological) + +AnnotationAssertion( "Exalpha Biological") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.exalpha.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Exalpha Biological") +ClassAssertion( ) + +# Individual: (Apogee Flow Systems) + +AnnotationAssertion( "Apogee Flow Systems") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.apogeeflow.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Apogee Flow Systems") +ClassAssertion( ) + +# Individual: (Exbio Antibodies) + +AnnotationAssertion( "Exbio Antibodies") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.exbio.cz/@2011/04/11") +AnnotationAssertion(rdfs:label "Exbio Antibodies") +ClassAssertion( ) + +# Individual: (Becton Dickinson (BD Biosciences)) + +AnnotationAssertion( "Becton Dickinson (BD Biosciences)") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.bdbiosciences.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Becton Dickinson (BD Biosciences)") +ClassAssertion( ) + +# Individual: (Dako Cytomation) + +AnnotationAssertion( "Dako Cytomation") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.dakousa.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Dako Cytomation") +ClassAssertion( ) + +# Individual: (Millipore) + +AnnotationAssertion( "Millipore") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.guavatechnologies.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Millipore") +ClassAssertion( ) + +# Individual: (Antigenix) + +AnnotationAssertion( "Antigenix") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.antigenix.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Antigenix") +ClassAssertion( ) + +# Individual: (Partec) + +AnnotationAssertion( "Partec") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.partec.de/@2011/04/11") +AnnotationAssertion(rdfs:label "Partec") +ClassAssertion( ) + +# Individual: (Beckman Coulter) + +AnnotationAssertion( "Beckman Coulter") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.beckmancoulter.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Beckman Coulter") +ClassAssertion( ) + +# Individual: (Advanced Instruments Inc. (AI Companies)) + +AnnotationAssertion( "Advanced Instruments Inc. (AI Companies)") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.aicompanies.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Advanced Instruments Inc. (AI Companies)") +ClassAssertion( ) + +# Individual: (Miltenyi Biotec) + +AnnotationAssertion( "Miltenyi Biotec") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.miltenyibiotec.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Miltenyi Biotec") +ClassAssertion( ) + +# Individual: (AES Chemunex) + +AnnotationAssertion( "AES Chemunex") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.aeschemunex.com/@2011/04/11") +AnnotationAssertion(rdfs:label "AES Chemunex") +ClassAssertion( ) + +# Individual: (Bentley Instruments) + +AnnotationAssertion( "Bentley Instruments") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://bentleyinstruments.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Bentley Instruments") +ClassAssertion( ) + +# Individual: (Invitrogen) + +AnnotationAssertion( "Invitrogen") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.invitrogen.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Invitrogen") +ClassAssertion( ) + +# Individual: (Luminex) + +AnnotationAssertion( "Luminex") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.luminexcorp.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Luminex") +ClassAssertion( ) + +# Individual: (CytoBuoy) + +AnnotationAssertion( "CytoBuoy") +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.cytobuoy.com/@2011/04/11") +AnnotationAssertion(rdfs:label "CytoBuoy") +ClassAssertion( ) + +# Individual: (Nimblegen) + +AnnotationAssertion( "Nimblegen") +AnnotationAssertion( "An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing."@en) +AnnotationAssertion( "Person: Jie Zheng") +AnnotationAssertion(rdfs:label "Nimblegen") +ClassAssertion( ) + +# Individual: (Pacific Biosciences) + +AnnotationAssertion( "Pacific Biosciences") +AnnotationAssertion( "An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution."@en) +AnnotationAssertion( "Person: Jie Zheng") +AnnotationAssertion(rdfs:label "Pacific Biosciences") +ClassAssertion( ) + +# Individual: (NanoString Technologies) + +AnnotationAssertion( "NanoString Technologies") +AnnotationAssertion( "An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules."@en) +AnnotationAssertion(rdfs:label "NanoString Technologies") +ClassAssertion( ) + +# Individual: (Thermo Fisher Scientific) + +AnnotationAssertion( "Thermo Fisher Scientific") +AnnotationAssertion( "An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific") +AnnotationAssertion(rdfs:label "Thermo Fisher Scientific") +ClassAssertion( ) + +# Individual: (G1: Well differentiated) + +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G1") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion(rdfs:label "G1: Well differentiated") +ClassAssertion( ) + +# Individual: (G2: Moderately differentiated) + +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G2") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion(rdfs:label "G2: Moderately differentiated") +ClassAssertion( ) + +# Individual: (G3: Poorly differentiated) + +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G3") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion(rdfs:label "G3: Poorly differentiated") +ClassAssertion( ) + +# Individual: (G4: Undifferentiated) + +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G4") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion(rdfs:label "G4: Undifferentiated") +ClassAssertion( ) + +# Individual: (G1 (Fuhrman)) + +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 1") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G1 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G2 (Fuhrman)) + +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 2") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G2 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G3 (Fuhrman)) + +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 3") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G3 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G4 (Fuhrman)) + +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 4") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G4 (Fuhrman)") +ClassAssertion( ) + +# Individual: (Low grade ovarian tumor) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Low grade") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "Low grade ovarian tumor") +ClassAssertion( ) + +# Individual: (High grade ovarian tumor) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "High grade") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "High grade ovarian tumor") +ClassAssertion( ) + +# Individual: (G1 (WHO)) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G1") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G1 (WHO)") +ClassAssertion( ) + +# Individual: (G2 (WHO)) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G2") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G2 (WHO)") +ClassAssertion( ) + +# Individual: (G3 (WHO)) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G3") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G3 (WHO)") +ClassAssertion( ) + +# Individual: (G4 (WHO)) + +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G4") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "G4 (WHO)") +ClassAssertion( ) + +# Individual: (pT0 (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT0 (colon)") +ClassAssertion( ) + +# Individual: (pTis (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pTis (colon)") +ClassAssertion( ) + +# Individual: (pT1 (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT1 (colon)") +ClassAssertion( ) + +# Individual: (pT2 (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT2 (colon)") +ClassAssertion( ) + +# Individual: (pT3 (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT3 (colon)") +ClassAssertion( ) + +# Individual: (pT4a (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT4a (colon)") +ClassAssertion( ) + +# Individual: (pT4b (colon)) + +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion(rdfs:label "pT4b (colon)") +ClassAssertion( ) + +# Individual: (pT0 (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT0 (lung)") +ClassAssertion( ) + +# Individual: (pTis (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pTis (lung)") +ClassAssertion( ) + +# Individual: (pT1 (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT1 (lung)") +ClassAssertion( ) + +# Individual: (pT1a (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT1a (lung)") +ClassAssertion( ) + +# Individual: (pT1b (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT1b (lung)") +ClassAssertion( ) + +# Individual: (pT2 (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT2 (lung)") +ClassAssertion( ) + +# Individual: (pT2a (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT2a (lung)") +ClassAssertion( ) + +# Individual: (pT2b (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT2b (lung)") +ClassAssertion( ) + +# Individual: (pT3 (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT3 (lung)") +ClassAssertion( ) + +# Individual: (pT4 (lung)) + +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion(rdfs:label "pT4 (lung)") +ClassAssertion( ) + +# Individual: (pT0 (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT0 (kidney)") +ClassAssertion( ) + +# Individual: (pT1 (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT1 (kidney)") +ClassAssertion( ) + +# Individual: (pT1a (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT1a (kidney)") +ClassAssertion( ) + +# Individual: (pT1b (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT1b (kidney)") +ClassAssertion( ) + +# Individual: (pT2 (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT2 (kidney)") +ClassAssertion( ) + +# Individual: (pT2a (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT2a (kidney)") +ClassAssertion( ) + +# Individual: (pT2b (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT2b (kidney)") +ClassAssertion( ) + +# Individual: (pT3 (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT3 (kidney)") +ClassAssertion( ) + +# Individual: (pT3a (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT3a (kidney)") +ClassAssertion( ) + +# Individual: (pT3b (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT3b (kidney)") +ClassAssertion( ) + +# Individual: (pT3c (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT3c (kidney)") +ClassAssertion( ) + +# Individual: (pT4 (kidney)) + +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion(rdfs:label "pT4 (kidney)") +ClassAssertion( ) + +# Individual: (pT0 (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT0 (ovary)") +ClassAssertion( ) + +# Individual: (pT1 (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT1 (ovary)") +ClassAssertion( ) + +# Individual: (pT1a (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT1a (ovary)") +ClassAssertion( ) + +# Individual: (pT1b (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT1b (ovary)") +ClassAssertion( ) + +# Individual: (pT1c (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT1c (ovary)") +ClassAssertion( ) + +# Individual: (pT2 (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT2 (ovary)") +ClassAssertion( ) + +# Individual: (pT2a (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT2a (ovary)") +ClassAssertion( ) + +# Individual: (pT2b (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT2b (ovary)") +ClassAssertion( ) + +# Individual: (pT2c (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT2c (ovary)") +ClassAssertion( ) + +# Individual: (pT3 (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT3 (ovary)") +ClassAssertion( ) + +# Individual: (pT3a (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT3a (ovary)") +ClassAssertion( ) + +# Individual: (pT3b (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT3b (ovary)") +ClassAssertion( ) + +# Individual: (pT3c (ovary)) + +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion(rdfs:label "pT3c (ovary)") +ClassAssertion( ) + +# Individual: (pN0 (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN0 (colon)") +ClassAssertion( ) + +# Individual: (pN1 (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN1 (colon)") +ClassAssertion( ) + +# Individual: (pN1a (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN1a (colon)") +ClassAssertion( ) + +# Individual: (pN1b (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN1b (colon)") +ClassAssertion( ) + +# Individual: (pN1c (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN1c (colon)") +ClassAssertion( ) + +# Individual: (pN2 (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN2 (colon)") +ClassAssertion( ) + +# Individual: (pN2a (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN2a (colon)") +ClassAssertion( ) + +# Individual: (pN2b (colon)) + +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion(rdfs:label "pN2b (colon)") +ClassAssertion( ) + +# Individual: (pN0 (lung)) + +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion(rdfs:label "pN0 (lung)") +ClassAssertion( ) + +# Individual: (pN1 (lung)) + +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion(rdfs:label "pN1 (lung)") +ClassAssertion( ) + +# Individual: (pN2 (lung)) + +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion(rdfs:label "pN2 (lung)") +ClassAssertion( ) + +# Individual: (pN3 (lung)) + +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion(rdfs:label "pN3 (lung)") +ClassAssertion( ) + +# Individual: (pN0 (kidney)) + +AnnotationAssertion( "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/") +AnnotationAssertion(rdfs:label "pN0 (kidney)") +ClassAssertion( ) + +# Individual: (pN1 (kidney)) + +AnnotationAssertion( "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/") +AnnotationAssertion(rdfs:label "pN1 (kidney)") +ClassAssertion( ) + +# Individual: (pN0 (ovary)) + +AnnotationAssertion( "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/") +AnnotationAssertion(rdfs:label "pN0 (ovary)") +ClassAssertion( ) + +# Individual: (pN1 (ovary)) + +AnnotationAssertion( "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/") +AnnotationAssertion(rdfs:label "pN1 (ovary)") +ClassAssertion( ) + +# Individual: (cM0 (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29") +AnnotationAssertion(rdfs:label "cM0 (colon)") +ClassAssertion( ) + +# Individual: (cM1 (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29") +AnnotationAssertion(rdfs:label "cM1 (colon)") +ClassAssertion( ) + +# Individual: (cM1a (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion(rdfs:label "cM1a (colon)") +ClassAssertion( ) + +# Individual: (cM1b (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion(rdfs:label "cM1b (colon)") +ClassAssertion( ) + +# Individual: (pM1 (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion(rdfs:label "pM1 (colon)") +ClassAssertion( ) + +# Individual: (pM1a (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion(rdfs:label "pM1a (colon)") +ClassAssertion( ) + +# Individual: (pM1b (colon)) + +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion(rdfs:label "pM1b (colon)") +ClassAssertion( ) + +# Individual: (cM0 (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "cM0 (lung)") +ClassAssertion( ) + +# Individual: (cM1 (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "cM1 (lung)") +ClassAssertion( ) + +# Individual: (cM1a (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "cM1a (lung)") +ClassAssertion( ) + +# Individual: (cM1b (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "cM1b (lung)") +ClassAssertion( ) + +# Individual: (pM1 (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "pM1 (lung)") +ClassAssertion( ) + +# Individual: (pM1a (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "pM1a (lung)") +ClassAssertion( ) + +# Individual: (pM1b (lung)) + +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion(rdfs:label "pM1b (lung)") +ClassAssertion( ) + +# Individual: (cM0 (kidney)) + +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion(rdfs:label "cM0 (kidney)") +ClassAssertion( ) + +# Individual: (cM1 (kidney)) + +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion(rdfs:label "cM1 (kidney)") +ClassAssertion( ) + +# Individual: (pM1 (kidney)) + +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion(rdfs:label "pM1 (kidney)") +ClassAssertion( ) + +# Individual: (cM0 (ovary)) + +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion(rdfs:label "cM0 (ovary)") +ClassAssertion( ) + +# Individual: (cM1 (ovary)) + +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion(rdfs:label "cM1 (ovary)") +ClassAssertion( ) + +# Individual: (pM1 (ovary)) + +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion(rdfs:label "pM1 (ovary)") +ClassAssertion( ) + +# Individual: (Occult Carcinoma (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Occult Carcinoma") +AnnotationAssertion( "http://www.medilexicon.com/dictionary/14371") +AnnotationAssertion(rdfs:label "Occult Carcinoma (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage 0 (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 0") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage 0 (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage I (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage I") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage I (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIA (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIB (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIC (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIC") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIC (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIA (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIIA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIB (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIIB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIC (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIC") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIIC (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IVA (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IVA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IVB (AJCC 7th)) + +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion(rdfs:label "Stage IVB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IA (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IA1 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IA1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IA2 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IA2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA"@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB1 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IB1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB2 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IB2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA1 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIA1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA2 (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIA2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIB (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIIA (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIIA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIIB (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IIIB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IVA (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IVA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IVB (FIGO)) + +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion(rdfs:label "Stage IVB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1 (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1A (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 1A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1B (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 1B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1C (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 1C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2 (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2A (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 2A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2B (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 2B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2C (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 2C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3 (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 3 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3A (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 3A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3B (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 3B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3C (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 3C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 4 (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 4") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage 4 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage Unknown (FIGO)) + +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage Unknown") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion(rdfs:label "Stage Unknown (FIGO)") +ClassAssertion( ) + +# Individual: (3: symptomatic in bed more than 50% of the day but not bed ridden) + +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "3: symptomatic in bed more than 50% of the day but not bed ridden") +ClassAssertion( ) + +# Individual: (2: symptomatic but in bed less than 50% of the day) + +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "2: symptomatic but in bed less than 50% of the day") +ClassAssertion( ) + +# Individual: (4: bed ridden) + +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "4: bed ridden") +ClassAssertion( ) + +# Individual: (0: asymptomatic) + +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "0: asymptomatic") +ClassAssertion( ) + +# Individual: (1: symptomatic but fully ambulatory) + +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "1: symptomatic but fully ambulatory") +ClassAssertion( ) + +# Individual: (100: asymptomatic) + +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is asymptomatic."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "100: asymptomatic") +ClassAssertion( ) + +# Individual: (80-90: symptomatic but fully ambulatory) + +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "80-90: symptomatic but fully ambulatory") +ClassAssertion( ) + +# Individual: (60-70: symptomatic but in bed less than 50% of the day) + +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "60-70: symptomatic but in bed less than 50% of the day") +ClassAssertion( ) + +# Individual: (40-50: symptomatic, in bed more than 50% of the day, but not bed ridden) + +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion(rdfs:label "40-50: symptomatic, in bed more than 50% of the day, but not bed ridden") +ClassAssertion( ) + +# Individual: (Oxford Nanopore Technologies) + +AnnotationAssertion( "Oxford Nanopore Technologies") +AnnotationAssertion( "An organization that is developing and selling nanopore sequencing products and is based in the UK."@en) +AnnotationAssertion( "James A. Overton") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies") +AnnotationAssertion(rdfs:label "Oxford Nanopore Technologies") +ClassAssertion( ) + +# Individual: (BioGents) + +AnnotationAssertion( "BioGents") +AnnotationAssertion( "An organization that manufactures mosquito traps and other mosquito control products."@en) +AnnotationAssertion( "John Judkins") +AnnotationAssertion( "WEB:https://eu.biogents.com/about-biogents/") +AnnotationAssertion(rdfs:label "BioGents") +ClassAssertion( ) + +# Individual: (Abbott) + +AnnotationAssertion( "Abbott") +AnnotationAssertion( "A manufacturer of rapid point-of-care assay devices."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://www.globalpointofcare.abbott/en/about.html") +AnnotationAssertion(rdfs:label "Abbott") +ClassAssertion( ) + +# Individual: (J. Mitra) + +AnnotationAssertion( "J. Mitra") +AnnotationAssertion( "A manufacturer of in vitro diagnostic assay kits in India."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://jmitra.co.in/about-us/") +AnnotationAssertion(rdfs:label "J. Mitra") +ClassAssertion( ) + +# Individual: (InBios) + +AnnotationAssertion( "InBios") +AnnotationAssertion( "A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://inbios.com/about/") +AnnotationAssertion(rdfs:label "InBios") +ClassAssertion( ) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "out of scope") +ClassAssertion( ) + +# Individual: (axiom holds for all times) + +AnnotationAssertion( "## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation") +AnnotationAssertion(rdfs:label "axiom holds for all times"@en) + + +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DifferentIndividuals( ) +DifferentIndividuals( ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/ms_terms.txt b/src/ontology/imports/ms_terms.txt new file mode 100644 index 0000000..8dcce9a --- /dev/null +++ b/src/ontology/imports/ms_terms.txt @@ -0,0 +1,3 @@ +http://purl.obolibrary.org/obo/MS_1000898 +http://purl.obolibrary.org/obo/MS_1000899 +http://purl.obolibrary.org/obo/MS_1000900 \ No newline at end of file diff --git a/src/ontology/imports/ncbitaxon_terms.txt b/src/ontology/imports/ncbitaxon_terms.txt new file mode 100644 index 0000000..2d7d2e9 --- /dev/null +++ b/src/ontology/imports/ncbitaxon_terms.txt @@ -0,0 +1,13 @@ +http://purl.obolibrary.org/obo/NCBITaxon_117571 +http://purl.obolibrary.org/obo/NCBITaxon_7742 +http://purl.obolibrary.org/obo/NCBITaxon_2759 +http://purl.obolibrary.org/obo/NCBITaxon_314146 +http://purl.obolibrary.org/obo/NCBITaxon_40674 +http://purl.obolibrary.org/obo/NCBITaxon_32523 +http://purl.obolibrary.org/obo/NCBITaxon_32524 +http://purl.obolibrary.org/obo/NCBITaxon_33154 +http://purl.obolibrary.org/obo/NCBITaxon_33213 +http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/NCBITaxon_10239 +http://purl.obolibrary.org/obo/NCBITaxon_2 +http://purl.obolibrary.org/obo/NCBITaxon_2157 \ No newline at end of file diff --git a/src/ontology/imports/nmrCV_terms.txt b/src/ontology/imports/nmrCV_terms.txt new file mode 100644 index 0000000..063c5e9 --- /dev/null +++ b/src/ontology/imports/nmrCV_terms.txt @@ -0,0 +1,748 @@ +http://nmrML.org/nmrCV#NMR:1000336 +http://nmrML.org/nmrCV#NMR:1400101 +http://nmrML.org/nmrCV#NMR:1000334 +http://nmrML.org/nmrCV#NMR:1000343 +http://nmrML.org/nmrCV#NMR:1000548 +http://nmrML.org/nmrCV#NMR:1000547 +http://nmrML.org/nmrCV#NMR:1400042 +http://nmrML.org/nmrCV#NMR:1000585 +http://nmrML.org/nmrCV#NMR:1000496 +http://nmrML.org/nmrCV#NMR:1000172 +http://nmrML.org/nmrCV#NMR:1400038 +http://nmrML.org/nmrCV#NMR:1000167 +http://nmrML.org/nmrCV#NMR:1000330 +http://nmrML.org/nmrCV#NMR:1400032 +http://nmrML.org/nmrCV#NMR:1000881 +http://nmrML.org/nmrCV#NMR:1002011 +http://nmrML.org/nmrCV#NMR:1400041 +http://nmrML.org/nmrCV#NMR:1000878 +http://nmrML.org/nmrCV#NMR:1400117 +http://nmrML.org/nmrCV#NMR:1000022 +http://nmrML.org/nmrCV#NMR:1000026 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b/src/ontology/imports/obi_terms.txt new file mode 100644 index 0000000..2351f49 --- /dev/null +++ b/src/ontology/imports/obi_terms.txt @@ -0,0 +1,123 @@ +http://purl.obolibrary.org/obo/OBI_0000245 +http://purl.obolibrary.org/obo/OBI_0001847 +http://purl.obolibrary.org/obo/OBI_9991118 +http://purl.obolibrary.org/obo/OBI_0000293 +http://purl.obolibrary.org/obo/OBI_0000295 +http://purl.obolibrary.org/obo/OBI_0000299 +http://purl.obolibrary.org/obo/OBI_0000312 +http://purl.obolibrary.org/obo/OBI_0002135 +http://purl.obolibrary.org/obo/OBI_0000011 +http://purl.obolibrary.org/obo/OBI_0100026 +http://purl.obolibrary.org/obo/OBI_0200000 +http://purl.obolibrary.org/obo/OBI_0000094 +http://purl.obolibrary.org/obo/OBI_0000652 +http://purl.obolibrary.org/obo/OBI_0000070 +http://purl.obolibrary.org/obo/OBI_0000047 +http://purl.obolibrary.org/obo/OBI_0001933 +http://purl.obolibrary.org/obo/OBI_0001909 +http://purl.obolibrary.org/obo/OBI_0001554 +http://purl.obolibrary.org/obo/OBI_0000066 +http://purl.obolibrary.org/obo/OBI_0000079 +http://purl.obolibrary.org/obo/OBI_0000272 +http://purl.obolibrary.org/obo/OBI_0000659 +http://purl.obolibrary.org/obo/OBI_0200169 +http://purl.obolibrary.org/obo/OBI_0302884 +http://purl.obolibrary.org/obo/OBI_0600014 +http://purl.obolibrary.org/obo/OBI_0100060 +http://purl.obolibrary.org/obo/OBI_0000968 +http://purl.obolibrary.org/obo/OBI_0000967 +http://purl.obolibrary.org/obo/OBI_0000932 +http://purl.obolibrary.org/obo/OBI_0000832 +http://purl.obolibrary.org/obo/OBI_0000984 +http://purl.obolibrary.org/obo/OBI_0000471 +http://purl.obolibrary.org/obo/OBI_0000838 +http://purl.obolibrary.org/obo/OBI_0500000 +http://purl.obolibrary.org/obo/OBI_0000115 +http://purl.obolibrary.org/obo/OBI_0000071 +http://purl.obolibrary.org/obo/OBI_0000443 +http://purl.obolibrary.org/obo/OBI_0200166 +http://purl.obolibrary.org/obo/OBI_0000427 +http://purl.obolibrary.org/obo/OBI_0000441 +http://purl.obolibrary.org/obo/OBI_0000451 +http://purl.obolibrary.org/obo/OBI_0000456 +http://purl.obolibrary.org/obo/OBI_0000639 +http://purl.obolibrary.org/obo/OBI_0100051 +http://purl.obolibrary.org/obo/OBI_0000662 +http://purl.obolibrary.org/obo/OBI_0000668 +http://purl.obolibrary.org/obo/OBI_0200168 +http://purl.obolibrary.org/obo/OBI_0000674 +http://purl.obolibrary.org/obo/OBI_0200181 +http://purl.obolibrary.org/obo/OBI_0000679 +http://purl.obolibrary.org/obo/OBI_0200170 +http://purl.obolibrary.org/obo/OBI_0000112 +http://purl.obolibrary.org/obo/OBI_0000744 +http://purl.obolibrary.org/obo/OBI_0000747 +http://purl.obolibrary.org/obo/OBI_0200186 +http://purl.obolibrary.org/obo/OBI_0000811 +http://purl.obolibrary.org/obo/OBI_0001404 +http://purl.obolibrary.org/obo/OBI_0001364 +http://purl.obolibrary.org/obo/OBI_0001834 +http://purl.obolibrary.org/obo/OBI_0200163 +http://purl.obolibrary.org/obo/OBI_0200089 +http://purl.obolibrary.org/obo/OBI_0600015 +http://purl.obolibrary.org/obo/OBI_0500002 +http://purl.obolibrary.org/obo/OBI_0000833 +http://purl.obolibrary.org/obo/OBI_0000417 +http://purl.obolibrary.org/obo/OBI_0001688 +http://purl.obolibrary.org/obo/OBI_0000846 +http://purl.obolibrary.org/obo/OBI_0000339 +http://purl.obolibrary.org/obo/OBI_0600024 +http://purl.obolibrary.org/obo/OBI_0600036 +http://purl.obolibrary.org/obo/OBI_0000750 +http://purl.obolibrary.org/obo/OBI_0000678 +http://purl.obolibrary.org/obo/OBI_0000681 +http://purl.obolibrary.org/obo/OBI_0001912 +http://purl.obolibrary.org/obo/OBI_0001938 +http://purl.obolibrary.org/obo/OBI_0000124 +http://purl.obolibrary.org/obo/OBI_0001937 +http://purl.obolibrary.org/obo/OBI_0000643 +http://purl.obolibrary.org/obo/OBI_0001931 +http://purl.obolibrary.org/obo/OBI_0000338 +http://purl.obolibrary.org/obo/OBI_0000067 +http://purl.obolibrary.org/obo/OBI_0000931 +http://purl.obolibrary.org/obo/OBI_0000437 +http://purl.obolibrary.org/obo/OBI_0000275 +http://purl.obolibrary.org/obo/OBI_0000686 +http://purl.obolibrary.org/obo/OBI_0000684 +http://purl.obolibrary.org/obo/OBI_0000740 +http://purl.obolibrary.org/obo/OBI_0000453 +http://purl.obolibrary.org/obo/OBI_0000806 +http://purl.obolibrary.org/obo/OBI_0000372 +http://purl.obolibrary.org/obo/OBI_0001930 +http://purl.obolibrary.org/obo/OBI_0000370 +http://purl.obolibrary.org/obo/OBI_0001305 +http://purl.obolibrary.org/obo/OBI_0001225 +http://purl.obolibrary.org/obo/OBI_0000175 +http://purl.obolibrary.org/obo/OBI_0001442 +http://purl.obolibrary.org/obo/OBI_0000791 +http://purl.obolibrary.org/obo/OBI_0200167 +http://purl.obolibrary.org/obo/OBI_0000425 +http://purl.obolibrary.org/obo/OBI_0200177 +http://purl.obolibrary.org/obo/OBI_0000314 +http://purl.obolibrary.org/obo/OBI_0001927 +http://purl.obolibrary.org/obo/OBI_0000086 +http://purl.obolibrary.org/obo/OBI_0000097 +http://purl.obolibrary.org/obo/OBI_0000181 +http://purl.obolibrary.org/obo/OBI_0000185 +http://purl.obolibrary.org/obo/OBI_0000250 +http://purl.obolibrary.org/obo/OBI_0000751 +http://purl.obolibrary.org/obo/OBI_0000789 +http://purl.obolibrary.org/obo/OBI_0000938 +http://purl.obolibrary.org/obo/OBI_0000963 +http://purl.obolibrary.org/obo/OBI_0001172 +http://purl.obolibrary.org/obo/OBI_0001352 +http://purl.obolibrary.org/obo/OBI_0001755 +http://purl.obolibrary.org/obo/OBI_0200036 +http://purl.obolibrary.org/obo/OBI_0200049 +http://purl.obolibrary.org/obo/OBI_0200094 +http://purl.obolibrary.org/obo/OBI_0200102 +http://purl.obolibrary.org/obo/OBI_0200111 +http://purl.obolibrary.org/obo/OBI_0300311 +http://purl.obolibrary.org/obo/OBI_0302900 +http://purl.obolibrary.org/obo/OBI_0500003 +http://purl.obolibrary.org/obo/OBI_0500020 \ No newline at end of file diff --git a/src/ontology/imports/ogms_terms.txt b/src/ontology/imports/ogms_terms.txt new file mode 100644 index 0000000..36b249b --- /dev/null +++ b/src/ontology/imports/ogms_terms.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/OGMS_0000023 \ No newline at end of file diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt new file mode 100644 index 0000000..262a82b --- /dev/null +++ b/src/ontology/imports/pato_terms.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/PATO_0000125 \ No newline at end of file diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt new file mode 100644 index 0000000..ccdf313 --- /dev/null +++ b/src/ontology/imports/pr_terms.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/PR_000000001 diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt new file mode 100644 index 0000000..f275a54 --- /dev/null +++ b/src/ontology/imports/ro_terms.txt @@ -0,0 +1,17 @@ +http://purl.obolibrary.org/obo/RO_0001900 +http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0000056 +http://purl.obolibrary.org/obo/RO_0000052 +http://purl.obolibrary.org/obo/RO_0000053 +http://purl.obolibrary.org/obo/RO_0000058 +http://purl.obolibrary.org/obo/RO_0000059 +http://purl.obolibrary.org/obo/RO_0000079 +http://purl.obolibrary.org/obo/RO_0000085 +http://purl.obolibrary.org/obo/RO_0000080 +http://purl.obolibrary.org/obo/RO_0000086 +http://purl.obolibrary.org/obo/RO_0000081 +http://purl.obolibrary.org/obo/RO_0000087 +http://purl.obolibrary.org/obo/RO_0001000 +http://purl.obolibrary.org/obo/RO_0001001 +http://purl.obolibrary.org/obo/RO_0001901 \ No newline at end of file diff --git a/src/ontology/imports/so_terms.txt b/src/ontology/imports/so_terms.txt new file mode 100644 index 0000000..2204880 --- /dev/null +++ b/src/ontology/imports/so_terms.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/SO_0000001 diff --git a/src/ontology/imports/uo_terms.txt b/src/ontology/imports/uo_terms.txt new file mode 100644 index 0000000..0c0bb8f --- /dev/null +++ b/src/ontology/imports/uo_terms.txt @@ -0,0 +1,21 @@ +http://purl.obolibrary.org/obo/UO_0000001 +http://purl.obolibrary.org/obo/UO_0000010 +http://purl.obolibrary.org/obo/UO_0000031 +http://purl.obolibrary.org/obo/UO_0000002 +http://purl.obolibrary.org/obo/UO_0000003 +http://purl.obolibrary.org/obo/UO_0000009 +http://purl.obolibrary.org/obo/UO_0000012 +http://purl.obolibrary.org/obo/UO_0000021 +http://purl.obolibrary.org/obo/UO_0000022 +http://purl.obolibrary.org/obo/UO_0000023 +http://purl.obolibrary.org/obo/UO_0000027 +http://purl.obolibrary.org/obo/UO_0000036 +http://purl.obolibrary.org/obo/UO_0000063 +http://purl.obolibrary.org/obo/UO_0000064 +http://purl.obolibrary.org/obo/UO_0000098 +http://purl.obolibrary.org/obo/UO_0000101 +http://purl.obolibrary.org/obo/UO_0000176 +http://purl.obolibrary.org/obo/UO_0000187 +http://purl.obolibrary.org/obo/UO_0000228 +http://purl.obolibrary.org/obo/UO_0000274 +http://purl.obolibrary.org/obo/UO_0000325 \ No newline at end of file diff --git a/src/ontology/msio-edit.owl b/src/ontology/msio-edit.owl new file mode 100644 index 0000000..e34a6e2 --- /dev/null +++ b/src/ontology/msio-edit.owl @@ -0,0 +1,2373 @@ +Prefix(:=) +Prefix(dc:=) +Prefix(obo:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(doap:=) +Prefix(foaf:=) +Prefix(msio:=) +Prefix(rdfs:=) +Prefix(skos:=) +Prefix(chebi:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) + + +Ontology( +Import() +Annotation(dc:contributor "Alejandra Gonzalez-Beltran"@en) +Annotation(dc:contributor "Andrew Lane"@en) +Annotation(dc:contributor "Hunter Moseley"@en) +Annotation(dc:contributor "Marta Cascante"@en) +Annotation(dc:contributor "Pedro Ramon de Atauri Carulla"@en) +Annotation(dc:contributor "Silvia Marin"@en) +Annotation(dc:contributor "Teresa Fan") +Annotation(dc:contributor "Vitaly Selivanov") +Annotation(dc:creator "Philippe Rocca-Serra") +Annotation(dc:description "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."@en) +Annotation(dc:license "http://creativecommons.org/licenses/by/3.0/") +Annotation(dc:title "Metabolomics Standards Initiative Ontology (MSIO)"@en) +Annotation(doap:bug-database "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues") +Annotation(doap:homepage "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO") + +Declaration(Class(obo:MSIO0000020)) +Declaration(Class(obo:MSIO_0000001)) +Declaration(Class(obo:MSIO_0000002)) +Declaration(Class(obo:MSIO_0000003)) +Declaration(Class(obo:MSIO_0000004)) +Declaration(Class(obo:MSIO_0000005)) +Declaration(Class(obo:MSIO_0000006)) +Declaration(Class(obo:MSIO_0000007)) +Declaration(Class(obo:MSIO_0000008)) +Declaration(Class(obo:MSIO_0000009)) +Declaration(Class(obo:MSIO_0000010)) +Declaration(Class(obo:MSIO_0000011)) +Declaration(Class(obo:MSIO_0000012)) +Declaration(Class(obo:MSIO_0000013)) +Declaration(Class(obo:MSIO_0000014)) +Declaration(Class(obo:MSIO_0000015)) +Declaration(Class(obo:MSIO_0000016)) +Declaration(Class(obo:MSIO_0000017)) +Declaration(Class(obo:MSIO_0000018)) +Declaration(Class(obo:MSIO_0000019)) +Declaration(Class(obo:MSIO_0000021)) +Declaration(Class(obo:MSIO_0000022)) +Declaration(Class(obo:MSIO_0000023)) +Declaration(Class(obo:MSIO_0000024)) +Declaration(Class(obo:MSIO_0000025)) +Declaration(Class(obo:MSIO_0000026)) +Declaration(Class(obo:MSIO_0000027)) +Declaration(Class(obo:MSIO_0000028)) +Declaration(Class(obo:MSIO_0000029)) +Declaration(Class(obo:MSIO_0000030)) +Declaration(Class(obo:MSIO_0000031)) +Declaration(Class(obo:MSIO_0000032)) +Declaration(Class(obo:MSIO_0000033)) +Declaration(Class(obo:MSIO_0000034)) +Declaration(Class(obo:MSIO_0000035)) +Declaration(Class(obo:MSIO_0000036)) +Declaration(Class(obo:MSIO_0000037)) +Declaration(Class(obo:MSIO_0000038)) +Declaration(Class(obo:MSIO_0000039)) +Declaration(Class(obo:MSIO_0000040)) +Declaration(Class(obo:MSIO_0000041)) +Declaration(Class(obo:MSIO_0000042)) +Declaration(Class(obo:MSIO_0000043)) +Declaration(Class(obo:MSIO_0000044)) +Declaration(Class(obo:MSIO_0000045)) +Declaration(Class(obo:MSIO_0000046)) +Declaration(Class(obo:MSIO_0000047)) +Declaration(Class(obo:MSIO_0000048)) +Declaration(Class(obo:MSIO_0000049)) +Declaration(Class(obo:MSIO_0000050)) +Declaration(Class(obo:MSIO_0000051)) +Declaration(Class(obo:MSIO_0000052)) +Declaration(Class(obo:MSIO_0000053)) +Declaration(Class(obo:MSIO_0000054)) +Declaration(Class(obo:MSIO_0000055)) +Declaration(Class(obo:MSIO_0000056)) +Declaration(Class(obo:MSIO_0000057)) +Declaration(Class(obo:MSIO_0000058)) +Declaration(Class(obo:MSIO_0000059)) +Declaration(Class(obo:MSIO_0000060)) +Declaration(Class(obo:MSIO_0000061)) +Declaration(Class(obo:MSIO_0000062)) +Declaration(Class(obo:MSIO_0000063)) +Declaration(Class(obo:MSIO_0000064)) +Declaration(Class(obo:MSIO_0000065)) +Declaration(Class(obo:MSIO_0000066)) +Declaration(Class(obo:MSIO_0000067)) +Declaration(Class(obo:MSIO_0000069)) +Declaration(Class(obo:MSIO_0000070)) +Declaration(Class(obo:MSIO_0000071)) +Declaration(Class(obo:MSIO_0000072)) +Declaration(Class(obo:MSIO_0000073)) +Declaration(Class(obo:MSIO_0000074)) +Declaration(Class(obo:MSIO_0000075)) +Declaration(Class(obo:MSIO_0000076)) +Declaration(Class(obo:MSIO_0000077)) +Declaration(Class(obo:MSIO_0000078)) +Declaration(Class(obo:MSIO_0000079)) +Declaration(Class(obo:MSIO_0000080)) +Declaration(Class(obo:MSIO_0000081)) +Declaration(Class(obo:MSIO_0000082)) +Declaration(Class(obo:MSIO_0000083)) +Declaration(Class(obo:MSIO_0000084)) +Declaration(Class(obo:MSIO_0000085)) +Declaration(Class(obo:MSIO_0000086)) +Declaration(Class(obo:MSIO_0000087)) +Declaration(Class(obo:MSIO_0000088)) +Declaration(Class(obo:MSIO_0000089)) +Declaration(Class(obo:MSIO_0000090)) +Declaration(Class(obo:MSIO_0000091)) +Declaration(Class(obo:MSIO_0000092)) +Declaration(Class(obo:MSIO_0000094)) +Declaration(Class(obo:MSIO_0000095)) +Declaration(Class(obo:MSIO_0000096)) +Declaration(Class(obo:MSIO_0000099)) +Declaration(Class(obo:MSIO_0000100)) +Declaration(Class(obo:MSIO_0000101)) +Declaration(Class(obo:MSIO_0000102)) +Declaration(Class(obo:MSIO_0000103)) +Declaration(Class(obo:MSIO_0000104)) +Declaration(Class(obo:MSIO_0000105)) +Declaration(Class(obo:MSIO_0000106)) +Declaration(Class(obo:MSIO_0000107)) +Declaration(Class(obo:MSIO_0000108)) +Declaration(Class(obo:MSIO_0000109)) +Declaration(Class(obo:MSIO_0000110)) +Declaration(Class(obo:MSIO_0000111)) +Declaration(Class(obo:MSIO_0000112)) +Declaration(Class(obo:MSIO_0000113)) +Declaration(Class(obo:MSIO_0000114)) +Declaration(Class(obo:MSIO_0000115)) +Declaration(Class(obo:MSIO_0000116)) +Declaration(Class(obo:MSIO_0000117)) +Declaration(Class(obo:MSIO_0000118)) +Declaration(Class(obo:MSIO_0000119)) +Declaration(Class(obo:MSIO_0000120)) +Declaration(Class(obo:MSIO_0000121)) +Declaration(Class(obo:MSIO_0000122)) +Declaration(Class(obo:MSIO_0000123)) +Declaration(Class(obo:MSIO_0000124)) +Declaration(Class(obo:MSIO_0000125)) +Declaration(Class(obo:MSIO_0000126)) +Declaration(Class(obo:MSIO_0000127)) +Declaration(Class(obo:MSIO_0000128)) +Declaration(Class(obo:MSIO_0000129)) +Declaration(Class(obo:MSIO_0000130)) +Declaration(Class(obo:MSIO_0000131)) +Declaration(Class(obo:MSIO_0000132)) +Declaration(Class(obo:MSIO_0000133)) +Declaration(Class(obo:MSIO_0000134)) +Declaration(Class(obo:MSIO_0000135)) +Declaration(Class(obo:MSIO_0000136)) +Declaration(Class(obo:MSIO_0000137)) +Declaration(Class(obo:MSIO_0000138)) +Declaration(Class(obo:MSIO_0000140)) +Declaration(Class(obo:MSIO_0000141)) +Declaration(Class(obo:MSIO_0000142)) +Declaration(Class(obo:MSIO_0000143)) +Declaration(Class(obo:MSIO_0000144)) +Declaration(Class(obo:MSIO_0000145)) +Declaration(Class(obo:MSIO_0000146)) +Declaration(Class(obo:MSIO_0000147)) +Declaration(Class(obo:MSIO_0000148)) +Declaration(Class(obo:MSIO_0000149)) +Declaration(Class(obo:MSIO_0000150)) +Declaration(Class(obo:MSIO_0000151)) +Declaration(Class(obo:MSIO_0000152)) +Declaration(Class(obo:MSIO_0000153)) +Declaration(Class(obo:MSIO_0000154)) +Declaration(Class(obo:MSIO_0000155)) +Declaration(Class(obo:MSIO_0000156)) +Declaration(Class(obo:MSIO_0000157)) +Declaration(Class(obo:MSIO_0000158)) +Declaration(Class(obo:MSIO_0000159)) +Declaration(Class(obo:MSIO_0000160)) +Declaration(Class(obo:MSIO_0000161)) +Declaration(Class(obo:MSIO_0000162)) +Declaration(Class(obo:MSIO_0000163)) +Declaration(Class(obo:MSIO_0000164)) +Declaration(Class(obo:MSIO_0000165)) +Declaration(Class(obo:MSIO_0000166)) +Declaration(Class(obo:MSIO_0000167)) +Declaration(Class(obo:MSIO_0000168)) +Declaration(Class(obo:MSIO_0000169)) +Declaration(Class(obo:MSIO_0000170)) +Declaration(Class(obo:MSIO_0000171)) +Declaration(Class(obo:MSIO_0000172)) +Declaration(Class(obo:MSIO_0000173)) +Declaration(Class(obo:MSIO_0000174)) +Declaration(Class(obo:MSIO_0000175)) +Declaration(Class(obo:MSIO_0000176)) +Declaration(Class(obo:MSIO_0000177)) +Declaration(Class(obo:MSIO_0000178)) +Declaration(Class(obo:MSIO_0000181)) +Declaration(Class(obo:MSIO_0000182)) +Declaration(Class(obo:MSIO_0000184)) +Declaration(Class(obo:MSIO_0000185)) +Declaration(Class(obo:MSIO_0000186)) +Declaration(Class(obo:MSIO_0000187)) +Declaration(Class(obo:MSIO_0000188)) +Declaration(Class(obo:MSIO_0000189)) +Declaration(Class(obo:MSIO_0000190)) +Declaration(Class(obo:MSIO_0000191)) +Declaration(Class(obo:MSIO_0000192)) +Declaration(Class(obo:MSIO_0000193)) +Declaration(Class(obo:MSIO_0000194)) +Declaration(Class(obo:MSIO_0000195)) +Declaration(Class(obo:MSIO_0000196)) +Declaration(Class(obo:MSIO_0000197)) +Declaration(NamedIndividual(obo:MSIO_0000068)) +Declaration(NamedIndividual(obo:MSIO_0000093)) +Declaration(NamedIndividual(obo:MSIO_0000097)) +Declaration(NamedIndividual(obo:MSIO_0000098)) +Declaration(AnnotationProperty(dc:contributor)) +Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:identifier)) +Declaration(AnnotationProperty(dc:language)) +Declaration(AnnotationProperty(dc:license)) +Declaration(AnnotationProperty(dc:publisher)) +Declaration(AnnotationProperty(dc:relation)) +Declaration(AnnotationProperty(dc:rights)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(dc:type)) +Declaration(AnnotationProperty(doap:bug-database)) +Declaration(AnnotationProperty(doap:revision)) +Declaration(AnnotationProperty(oboInOwl:id)) +Declaration(AnnotationProperty(oboInOwl:shorthand)) +Declaration(AnnotationProperty(skos:note)) +############################ +# Annotation Properties +############################ + +# Annotation Property: doap:homepage (doap:homepage) + +AnnotationAssertion(rdfs:isDefinedBy doap:homepage ) + + +############################ +# Object Properties +############################ + +# Object Property: obo:MSIO_0000179 (is isotopomer of) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000179 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000179 "a chemical entity is said to be an isotopomer of another one if it has the same number of each isotopic atom but differs in their positions. isotopomer is a contraction of isotopic isomer"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000179 "CH2DCH=0 is isotopomer of CH3CD=0"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000179 "IUPAC compendium of chemical terminology (2nd edition, 1997)"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000179 "is isotopomer of"@en) + +# Object Property: obo:MSIO_0000180 (is isotopologue of) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000180 "CH4 is isotopologue of CH3D which is isotopologue of CH2D2"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000180 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000180 "a molecular entity which differs only in isotopic composition (i.e the number of isotopic substitution differs but the overall chemical structure is unchanged) is said to be an isotologue"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000180 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000180 "IUPAC compendium of chemical terminology (2nd edition, 1997)"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000180 "is isotopologue of") + +# Object Property: obo:MSIO_0000183 (manufactured by) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000183 "A relation associating a product to its manufacturer."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000183 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000183 "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label obo:MSIO_0000183 "manufactured by"@en) +SubObjectPropertyOf(obo:MSIO_0000183 owl:topObjectProperty) + + +############################ +# Classes +############################ + +# Class: obo:MSIO0000020 (openFlux2) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO0000020 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO0000020 "OpenFLUX2 is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes. OpenFlux2 is an expanded version of OpenFLUX to support analysis of parallel labeling experiments (PLE) data, i.e. those experiments using several different tracers concomitantly.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO0000020 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO0000020 "https://doi.org/10.1186/s12934-014-0152-x") +AnnotationAssertion(rdfs:label obo:MSIO0000020 "openFlux2") +SubClassOf(obo:MSIO0000020 obo:IAO_0000010) + +# Class: obo:MSIO_0000001 (chemical reaction) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000001 "2H2O -> 2H2+ O2") +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000001 "a process which uses or consumes chemical/molecular entities to generate other molecular entities"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000001 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000001 "adapted from wikipedia: +https://en.wikipedia.org/wiki/Chemical_reaction +last accessed: 2018-01-11") +AnnotationAssertion(rdfs:label obo:MSIO_0000001 "chemical reaction"@en) +SubClassOf(obo:MSIO_0000001 obo:BFO_0000015) + +# Class: obo:MSIO_0000002 (buffer role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000002 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000002 "buffer role is a role played by a chemical solution to dampens pH variation"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000002 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000002 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000002 "buffer role"@en) +SubClassOf(obo:MSIO_0000002 obo:BFO_0000023) + +# Class: obo:MSIO_0000003 (derivatization agent role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000003 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000003 "derivatization agent role is a role played by a chemical entity involved in a chemical reaction known as derivatization whereby another chemical entity is augmented, but not altered otherwise, with groups specify to the chemical entity acting as a derivatization agent."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000003 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000003 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000003 "derivatization agent role"@en) +SubClassOf(obo:MSIO_0000003 obo:BFO_0000023) + +# Class: obo:MSIO_0000004 (external standard role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000004 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000004 "external standard role is a role played by a material entity used as a reference point for signal acquisition. this is a type of positive control role"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000004 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000004 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000004 "external standard role"@en) +SubClassOf(obo:MSIO_0000004 obo:MSIO_0000008) + +# Class: obo:MSIO_0000005 (internal standard role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000005 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000005 "internal standard role is a role played by a chemical entity added in known amount to an analytical sample"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000005 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000005 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000005 "internal standard role"@en) +SubClassOf(obo:MSIO_0000005 obo:MSIO_0000008) + +# Class: obo:MSIO_0000006 (long term reference role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000006 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000006 "long term reference role is a role played by a material entity known for its stability to provide the means to compare across sets of acquisitions"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000006 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000006 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000006 "long term reference role"@en) +SubClassOf(obo:MSIO_0000006 obo:BFO_0000023) + +# Class: obo:MSIO_0000007 (negative control role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000007 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000007 "positive control role is a role played by a material entity in the context of analytical work to provide no signal or a signal as close to baseline as technically possible (within the limits of detection) thereby providing a reference point for the noise and indicative that the detectors and signal acquisition system operate nominally."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000007 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000007 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000007 "negative control role"@en) +SubClassOf(obo:MSIO_0000007 obo:BFO_0000023) + +# Class: obo:MSIO_0000008 (positive control role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000008 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000008 "positive control role is a role played by a material entity in the context of analytical work to provide a signal of known intensity indicative that the detectors and signal acquisition system operate nominally."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000008 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000008 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000008 "positive control role"@en) +SubClassOf(obo:MSIO_0000008 obo:BFO_0000023) + +# Class: obo:MSIO_0000009 (solvent role) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000009 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000009 "solvent role is a role played by a chemical entity present in a solution and providing the solvatation activity to other compounds, the solutes."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000009 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000009 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000009 "solvent role"@en) +SubClassOf(obo:MSIO_0000009 obo:BFO_0000023) + +# Class: obo:MSIO_0000010 (AbsoluteIDQ p150 Kit) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000010 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000010 "AbsoluteIDQ p150 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 163 distinct molecular entities with quantitative accuracy on human plasma samples."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000010 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000010 "http://www.biocrates.com/products/research-products/absoluteidq-p150-kit"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000010 "AbsoluteIDQ p150 Kit"@en) +SubClassOf(obo:MSIO_0000010 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000010 ObjectSomeValuesFrom(obo:OBI_0000295 obo:MSIO_0000100)) +SubClassOf(obo:MSIO_0000010 ObjectHasValue(obo:MSIO_0000183 obo:MSIO_0000068)) + +# Class: obo:MSIO_0000011 (AbsoluteIDQ p180 Kit) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000011 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000011 "AbsoluteIDQ p180 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 188 distinct endogenous molecular entities with quantitative accuracy from 5 different compound classes (i.e. acylcarnitines, amino acids, hexoses, phospho- and sphingolipids and biogenic amines). The assay requires very small sample amounts (10 μL) and shows excellent reproducibility."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000011 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000011 "http://www.biocrates.com/products/research-products/absoluteidq-p180-kit"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000011 "AbsoluteIDQ p180 Kit"@en) +SubClassOf(obo:MSIO_0000011 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000011 ObjectSomeValuesFrom(obo:OBI_0000295 obo:MSIO_0000100)) +SubClassOf(obo:MSIO_0000011 ObjectHasValue(obo:MSIO_0000183 obo:MSIO_0000068)) + +# Class: obo:MSIO_0000012 (AbsoluteIDQ Stero17 Kit) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000012 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000012 "AbsoluteIDQ Stero17 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling (identification and quantification) of 17 steroid hormones (sex steroids, mineralocorticoids, glucocorticoids)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000012 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000012 "http://www.biocrates.com/products/research-products/absoluteidq-p150-kit"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000012 "AbsoluteIDQ Stero17 Kit"@en) +SubClassOf(obo:MSIO_0000012 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000012 ObjectSomeValuesFrom(obo:OBI_0000295 obo:MSIO_0000100)) +SubClassOf(obo:MSIO_0000012 ObjectHasValue(obo:MSIO_0000183 obo:MSIO_0000068)) + +# Class: obo:MSIO_0000013 (AbsoluteIDQ p400 Kit) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000013 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000013 "AbsoluteIDQ p400 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 400 distinct molecular entities with quantitative accuracy on human plasma samples."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000013 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000013 "http://www.biocrates.com/products/research-products/absoluteidq-p400-hr-kit"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000013 "AbsoluteIDQ p400 Kit"@en) +SubClassOf(obo:MSIO_0000013 obo:BFO_0000040) + +# Class: obo:MSIO_0000014 (ammonium bicarbonate buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000014 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000014 "ammonium bicarbonate is kind of buffer solution where the weak base is ammonium and the weak acid carbonic acid."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000014 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000014 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000014 "ammonium bicarbonate buffer"@en) +SubClassOf(obo:MSIO_0000014 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000014 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000002)) + +# Class: obo:MSIO_0000015 (buffer) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000015 "the bicarbonate buffering system is used to regulate the pH of blood."@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000015 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000015 "A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000015 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000015 "https://en.wikipedia.org/wiki/Buffer_solution"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000015 "buffer"@en) +EquivalentClasses(obo:MSIO_0000015 ObjectIntersectionOf(obo:BFO_0000040 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000002))) +SubClassOf(obo:MSIO_0000015 obo:BFO_0000040) + +# Class: obo:MSIO_0000016 (dilution series reference) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000016 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000016 "a dilution series sample is a material entity which is part of a collection of such materials, each defined by its dilution factor with respect to a stock solution of reference sample. Dilution series samples are used to assess the linearity of the signal acquisition by providing a set of expected and known quantities."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000016 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000016 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000016 "dilution series reference"@en) +SubClassOf(obo:MSIO_0000016 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000016 ObjectSomeValuesFrom(obo:OBI_0000295 ObjectUnionOf(obo:MSIO_0000084 obo:MSIO_0000085))) + +# Class: obo:MSIO_0000017 (fetal bovine serum) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000017 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000017 "Fetal bovine serum (FBS) or fetal calf serum (spelled foetal in Commonwealth English) is a material entity which correspsonds to the blood fraction remaining after the natural coagulation of blood, followed by centrifugation to remove any remaining red blood cells."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000017 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000017 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000017 "https://en.wikipedia.org/wiki/Fetal_bovine_serum"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000017 "fetal bovine serum"@en) +SubClassOf(obo:MSIO_0000017 obo:BFO_0000040) + +# Class: obo:MSIO_0000018 (HEPES buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000018 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000018 "HEPES buffer is a buffer which uses HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) as a zwitterionic organic chemical buffering agent ."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000018 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000018 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000018 "HEPES buffer"@en) +SubClassOf(obo:MSIO_0000018 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000018 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000002)) + +# Class: obo:MSIO_0000019 (long term reference) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000019 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000019 "a pooled sample made from fractions from samples collected from large, study independent collection of samples with the purpose of serving as a reference for quality control purpose. Long Term Reference Samples maybe used in ring trials to check cross facility data acquisition consistency but also to enable data integration, irrespective of data acquisition platform or study context but providing a single point of reference against which to normalize. + +purpose: Inter study variability(within a core facility)"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000019 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000019 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000019 "LTR"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000019 "biological pool (inter) [CEA]"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000019 "biological pool [MASTR-MS]"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000019 "inter study QC"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000019 "H2020 PhenoMenal"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000019 "long term reference"@en) +SubClassOf(obo:MSIO_0000019 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000019 ObjectSomeValuesFrom(obo:OBI_0000295 ObjectUnionOf(obo:MSIO_0000084 obo:MSIO_0000085))) + +# Class: obo:MSIO_0000021 (PBS buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000021 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000021 "Phosphated buffer saline (PBS) buffer is a buffer which is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and potassium dihydrogen phosphate."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000021 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000021 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000021 "https://en.wikipedia.org/wiki/Phosphate-buffered_saline"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000021 "PBS buffer"@en) +SubClassOf(obo:MSIO_0000021 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000021 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000002)) + +# Class: obo:MSIO_0000022 (quality control material) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000022 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000022 "quality control material (qc material) is a material entity which is used for the purpose to quality control processes such as assessing unwanted source of variations during signal acquisitions. Typically, these materials are known compounds or mixture of compounds introduced in known quantities into test samples or run as is, diluted from stock to provide reference measurements at fixed temporal intervals."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000022 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000022 "QC material"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000022 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000022 "quality control material"@en) +SubClassOf(obo:MSIO_0000022 obo:BFO_0000040) + +# Class: obo:MSIO_0000023 (reference compound) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000023 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000023 "a reference compound is a chemical entity of know origin, formula and established spectral fingerprint added to a solution of unknown component in known quantities in order to provide a basis (hence the term reference) with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000023 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000023 "pure standard"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000023 "reference material"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000023 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000023 "reference compound"@en) +SubClassOf(obo:MSIO_0000023 obo:BFO_0000040) + +# Class: obo:MSIO_0000024 (reference compound mix) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000024 "NIST reference material: +https://www.nist.gov/publications/certification-standard-reference-materialr-968f-fat-soluble-vitamins-frozen-human-serum"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000024 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000024 "a reference compound mix is a material entity which consists of composite solution of several molecular entities acting as reference compound and present in known quantity in the mixture, with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000024 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000024 "pure standard mix"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000024 "reference material mix"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000024 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000024 "reference compound mix"@en) +SubClassOf(obo:MSIO_0000024 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000024 ObjectSomeValuesFrom(obo:BFO_0000051 obo:MSIO_0000023)) + +# Class: obo:MSIO_0000025 (sample preparation blank) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000025 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000025 "a material entity corresponding to a sample containing no biological sample, which undergoes all laboratory process of preparation as used for test samples and used as a negative control to evaluate contamination effect and artefacts caused by reactions occurring during the sample preparation steps of test samples."@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000025 "method blank"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000025 "method reference"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000025 "sample preparation blank"@en) +SubClassOf(obo:MSIO_0000025 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000025 ObjectSomeValuesFrom(obo:OBI_0000295 ObjectUnionOf(obo:MSIO_0000084 obo:MSIO_0000085))) + +# Class: obo:MSIO_0000026 (solvent blank) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000026 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000026 "a material entity corresponding to ‘solvent’ (mobile phase in chromatography context) only, containing no biological sample and used as a negative control to evaluate carry over effect between injections of test samples."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000026 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000026 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000026 "normal blank [Leiden]"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000026 "solvent blank"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000026 "solvent blank"@en) +SubClassOf(obo:MSIO_0000026 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000026 ObjectSomeValuesFrom(obo:OBI_0000295 ObjectUnionOf(obo:MSIO_0000084 obo:MSIO_0000085))) + +# Class: obo:MSIO_0000027 (study reference material) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000027 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000027 "a study reference sample is a pool made up of aliquots from all the sample collected in a given study. It is meant to be used to monitor intra study variability, also known as within study variability of the signal acquisition, for instance between batches of such data acquisition."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000027 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000027 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000027 "SR"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000027 "iQC - internal quality control [Imperial College London]"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000027 "study reference") +AnnotationAssertion(rdfs:label obo:MSIO_0000027 "study reference material"@en) +SubClassOf(obo:MSIO_0000027 obo:BFO_0000040) +SubClassOf(obo:MSIO_0000027 ObjectSomeValuesFrom(obo:OBI_0000295 ObjectUnionOf(obo:MSIO_0000084 obo:MSIO_0000085))) + +# Class: obo:MSIO_0000028 (carrier gas) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000028 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000028 "a carrier gas is a chemical entity in gaseous phase with is used for eluting chemical compound in a gas chromatography process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000028 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000028 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000028 "carrier gas"@en) +SubClassOf(obo:MSIO_0000028 obo:CHEBI_23367) + +# Class: obo:MSIO_0000029 (derivatization agent) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000029 "tert-Butyldimethylsilyl chloride is a derivatization agent"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000029 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000029 "a derivatization agent is a chemical entity which is used in a material combination process known as derivatization and which consists in adding chemical groups to a molecule in an attempt to make it more volatile and therefore amenable to gas-chromatography mass spectrometry."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000029 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000029 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000029 "derivatization agent"@en) +EquivalentClasses(obo:MSIO_0000029 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000003)) +SubClassOf(obo:MSIO_0000029 obo:CHEBI_23367) + +# Class: obo:MSIO_0000030 (quaternary ammonium dodecyl aminooxy reagent) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000030 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000030 ""@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000030 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000030 "QDA reagent"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000030 ""@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000030 "quaternary ammonium dodecyl aminooxy reagent"@en) +SubClassOf(obo:MSIO_0000030 obo:MSIO_0000029) + +# Class: obo:MSIO_0000031 (isotopic tracer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000031 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000031 "an isotopic tracer is a molecular entity whose atoms may have entirely or partially replaced with isotopes of the normally occuring element and which can be distinguished from naturally occuring molecular entity through mass analysis or nucleic magnetic resonance analysis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000031 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000031 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000031 "isotopic tracer"@en) +EquivalentClasses(obo:MSIO_0000031 ObjectSomeValuesFrom(obo:OBI_0000312 obo:MSIO_0000118)) +SubClassOf(obo:MSIO_0000031 obo:CHEBI_23367) + +# Class: obo:MSIO_0000032 (positionally labeled isotopic tracer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000032 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000032 "a specificly labeled isotopic tracer is an isotopic tracer where only specific positions on the backbone have been replaced with an isotopic atom. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000032 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000032 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000032 "positionally labeled isotopic tracer"@en) +SubClassOf(obo:MSIO_0000032 obo:MSIO_0000031) + +# Class: obo:MSIO_0000033 (uniformly labeled isotopic tracer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000033 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000033 "uniformly labeled isotopic tracer is an isotopic tracer where all atoms of the backbone are replaced with the same isotope. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000033 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000033 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000033 "uniformly labeled isotopic tracer"@en) +SubClassOf(obo:MSIO_0000033 obo:MSIO_0000031) + +# Class: obo:MSIO_0000034 (isotopologue) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000034 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000034 "A single isotopologue represents a set of mass-equivalent isotopomers. It is therefore a set of chemicals representing molecules of the same chemical entity and same isotopic composition. Isotopologue can be monitored using mass spectrometry but only NMR spectroscopy can discriminate between positional isotopomer."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000034 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000034 "adapted from IUPAC nomenclature"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000034 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000034 "isotopologue"@en) +SubClassOf(obo:MSIO_0000034 obo:CHEBI_23367) + +# Class: obo:MSIO_0000035 (openFlux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000035 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000035 "OpenFLUX is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000035 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000035 " +https://www.ncbi.nlm.nih.gov/pubmed/19409084"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000035 "openFlux"@en) +SubClassOf(obo:MSIO_0000035 obo:IAO_0000010) + +# Class: obo:MSIO_0000036 (isotopomer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000036 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000036 "a mass isotopomer (short for isotopic isomer) is a compound which differ from another one only by the position of an isotopic substitution in the molecular backbone. +One in a collection of isomers with the same number of each isotope of each element but differing in their positions within the chemical structure."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000036 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000036 "isotopic isomer"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000036 "mass isotopomer") +AnnotationAssertion(dc:contributor obo:MSIO_0000036 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000036 "isotopomer"@en) +SubClassOf(obo:MSIO_0000036 obo:CHEBI_23367) + +# Class: obo:MSIO_0000037 (solvent) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000037 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000037 "a solvent is a chemical entity playing a solvent role in a solution."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000037 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000037 obo:IAO_0000226) +AnnotationAssertion(rdfs:label obo:MSIO_0000037 "solvent"@en) +EquivalentClasses(obo:MSIO_0000037 ObjectIntersectionOf(obo:CHEBI_23367 ObjectSomeValuesFrom(obo:RO_0000087 obo:MSIO_0000009))) + +# Class: obo:MSIO_0000038 (uniformly-labeled [U-13C] glucose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000038 obo:IAO_0000226) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000038 "A non-radioactive, glucose molecule in which all six carbons are substituted with stable carbon 13 (13C) isotope, with potential imaging application or fluxomics studies. + +CAS RN 110187-42-3"@en) +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000038 "submit to CHEBI"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000038 "Philippe Rocca-Serra"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000038 "uniformly-labeled [U-13C] glucose"@en) +AnnotationAssertion(rdfs:seeAlso obo:MSIO_0000038 "http://www.cancer.gov/drugdictionary?cdrid=739239"@en) +SubClassOf(obo:MSIO_0000038 obo:CHEBI_23367) +SubClassOf(obo:MSIO_0000038 ObjectSomeValuesFrom(obo:OBI_0000312 obo:MSIO_0000120)) + +# Class: obo:MSIO_0000039 (partial isotopomer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000039 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000039 "an isotopomer where the isotopic content of specific atoms is known for a part of the molecule") +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000039 "should it be a relation or a class?"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000039 "Philippe Rocca-Serra"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000039 "partial isotopomer"@en) +SubClassOf(obo:MSIO_0000039 obo:CHEBI_23367) + +# Class: obo:MSIO_0000040 (metabolic flux unit) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000040 "metabolic flux unit is a measurement unit datum used to qualify a metabolic flux. It is therefore an amount of matter over a temporal interval."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000040 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000040 "Philippe Rocca-Serra for the COSMOS-Fluxomics Ontology (CFO)"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000040 "metabolic flux unit"@en) +SubClassOf(obo:MSIO_0000040 obo:IAO_0000003) +SubClassOf(obo:MSIO_0000040 ObjectSomeValuesFrom(obo:IAO_0000219 obo:MSIO_0000150)) + +# Class: obo:MSIO_0000041 (micromolar per milligram of protein per hour) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000041 "micromolar per milligram of protein per hour is a unit used to report metabolic fluxes. it denotes a measurement indicative of an amount of material over a period of time and normalized to the amount of protein present in the cellular fraction under consideration"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000041 "Philippe Rocca-Serra +"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000041 "umol mg prot-1 hr-1"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000041 "micromolar per milligram of protein per hour"@en) +SubClassOf(obo:MSIO_0000041 obo:MSIO_0000040) + +# Class: obo:MSIO_0000042 (13cflux2) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000042 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000042 "c13Fluc2 is a software suite of applications for the detailed quantification of intracellular (quasi) steady-state fluxes as explored by 13C-based metabolic flux analysis. The tool is developed and maintained by W. Wiechert at the Institute of Bio- and Geosciences, IBG-1: Biotechnology and JARA High Performance Computing, Forschungszentrum, Julich GmbH, 52428 Julich, Germany."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000042 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000042 " +Weitzel M, Nöh K, Dalman T, Niedenführ S, Stute B, Wiechert W +13CFLUX2 - High-Performance Software Suite for 13C-Metabolic Flux Analysis +Bioinformatics 2012 +doi: 10.1093/bioinformatics/bts646"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000042 "http://www.13cflux.net/13cflux2/"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000042 "13cflux2"@en) +SubClassOf(obo:MSIO_0000042 obo:IAO_0000010) + +# Class: obo:MSIO_0000043 (C13) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000043 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000043 "C13 is a tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments. The underlying approach is metabolic flux analysis based on stationary carbon isotope labelling experiments, using fractional enrichment data. The mathematical framework adopted herein is the one developed by Wiechert and de Graaf (1997). +It is developed and maintained at the Chalmers University of Technology, Department of Chemical and Biological Engineering, Systems Biology group , Kemivägen 10 412 96 Göteborg, Sweden."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000043 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000043 "http://129.16.106.142/tools.php?c=c13"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000043 "C13"@en) +SubClassOf(obo:MSIO_0000043 obo:IAO_0000010) + +# Class: obo:MSIO_0000044 (fiatFlux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000044 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000044 "An intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms. FiatFlux is written in Matlab"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000044 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000044 "http://www.ncbi.nlm.nih.gov/pubmed/16122385"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000044 "fiatFlux"@en) +SubClassOf(obo:MSIO_0000044 obo:IAO_0000010) + +# Class: obo:MSIO_0000045 (Fluxomer Iterative Algorithm) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000045 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000045 "FIA is a software written in python, implementing the FIA (Fluxomer Iterative Algorithm) - a new effective method for 13C metabolic fluxes (tracer) experiments analysis. It is developed by Orr Srour, Jamey D. Young and Yonina C. Eldar at the Technion, Israel Institute of Technology"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000045 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000045 "FIA"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000045 "https://doi.org/10.1186/1752-0509-5-129") +AnnotationAssertion(rdfs:label obo:MSIO_0000045 "Fluxomer Iterative Algorithm"@en) +SubClassOf(obo:MSIO_0000045 obo:IAO_0000010) + +# Class: obo:MSIO_0000046 (iMAT) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000046 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000046 "iMAT is a software integrating transcriptomic and proteomic data with genome-scale metabolic network models to predict enzyme metabolic flux. The tool is developed by Tomer Shlomi at The Isreal Institute of Technology"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000046 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000046 "Integrative Metabolic Analysis Tool"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000046 "Bioinformatics (2010) 26 (24): 3140-3142. +https://doi.org/10.1093/bioinformatics/btq602"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000046 "http://www.cs.technion.ac.il/~tomersh/methods.html"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000046 "iMAT"@en) +SubClassOf(obo:MSIO_0000046 obo:IAO_0000010) + +# Class: obo:MSIO_0000047 (INCA) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000047 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000047 "INCA: a computational platform for isotopically non-stationary metabolic flux analysis, Jamey D. Young. Bioinformatics, first published online January 11, 2014. +INCA is a software package that can perform both steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and elementary metabolite unit balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000047 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000047 "Isotopomer Network Compartmental Analysis"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000047 "http://www.ncbi.nlm.nih.gov/pubmed/24413674"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000047 "INCA"@en) +SubClassOf(obo:MSIO_0000047 obo:IAO_0000010) +SubClassOf(obo:MSIO_0000047 ObjectSomeValuesFrom(obo:OBI_0000295 obo:MSIO_0000128)) + +# Class: obo:MSIO_0000048 (iso2flux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000048 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000048 "Iso2Flux is a Python-based flux analysis software that allows to perform 13C Metabolic Flux Analysis on a sub-network of a large scale model. Iso2flux uses constraint-based modelling to compute steady state fluxes across a large metabolic network and uses such flxues to predict 13C distribution across a subser of the newtork. Then, given a set of 13C data Iso2flux can iteratively find the steady state flux distributions that are most consistent with such fluxes. + +the source code is available from: https://github.com/cfoguet/iso2flux"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000048 "http://portal.phenomenal-h2020.eu/app-library/iso2flux"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000048 "https://github.com/cfoguet/iso2flux"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000048 "Pedro de Atauri"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000048 "Vitaly Selivanov"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000048 "iso2flux"@en) +SubClassOf(obo:MSIO_0000048 obo:IAO_0000010) + +# Class: obo:MSIO_0000049 (isodyn) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000049 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000049 "“Isodyn” is a C++-program that performs an analysis of stable isotope tracer data to assess metabolic flux profiles in living cells. Isodyn simulates the dynamics of isotopic isomer (isotopomer) distribution in central metabolic pathways, and, by changing its parameters, which reflect the characteristics of corresponding biochemical reactions, fit the simulated dynamics of mass isotopomers to that observed experimentally. The simulated metabolic fluxes that correspond to the best fit are assumed to reproduce the real fluxes in the analyzed biological object and conditions. Isodyn contains tools that check the goodness of fit and perform a statistical analysis of obtained metabolic fluxes. + +the source code is available from: https://github.com/seliv55/isodyn"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000049 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000049 "http://portal.phenomenal-h2020.eu/app-library/isodyn"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000049 "Pedro de Atauri"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000049 "Vitaly Selivanov"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000049 "isodyn"@en) +SubClassOf(obo:MSIO_0000049 obo:IAO_0000010) + +# Class: obo:MSIO_0000050 (isodesign) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000050 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000050 "IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. + +The software is available from: +http://metasys.insa-toulouse.fr/software/isodes/"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000050 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000050 "https://doi.org/10.1002/bit.24997"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000050 "isodesign"@en) +SubClassOf(obo:MSIO_0000050 obo:IAO_0000010) + +# Class: obo:MSIO_0000051 (metran) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000051 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000051 "Metran is a software for Metabolic Flux Analysis implementing the Elementary Metabolite Units. + +Metabolic Flux Analysis (MFA) has emerged as a tool of great significance for metabolic engineering and quantitative cell physiology. An important limitation of MFA, as carried out via stable isotope labeling and GC-MS measurements, is the large number of isotopomer/cumomer equations that need to be solved, especially when multiple isotopic tracers are used for the labeling of the system. This restriction reduces the ability of MFA to fully utilize the power of multiple isotopic tracers in elucidating the physiology of realistic situations comprising complex bioreaction networks. + +To address this limitation, we have developed a novel framework for modeling of isotopic tracer distributions that significantly reduces the number of variables, without any loss of information. The EMU framework is based on a highly efficient decomposition method that identifies the minimum amount of information needed to simulate isotopic labeling within a reaction network using the knowledge of atomic transitions occurring in the network reactions. The functional units generated by the decomposition algorithm, called elementary metabolite units (EMUs), form the new basis for generating system equations that describe the relationship between fluxes and isotopomer abundances. + +The EMU decomposition algorithm is completely unsupervised and converges within seconds even for very genome-wide network models. Isotopomer abundances simulated using the EMU framework are identical to those obtained using the isotopomer and cumomer frameworks, however, requiring significantly less computation time. For a typical carbon labeling system the total number of equations that needs to be solved is reduced by one order-of-magnitude (100s EMUs vs. 1000s cumomers). As such, the EMU framework is most efficient for the analysis of labeling by multiple isotopic tracers. For example, the analysis of gluconeogenesis network model with 2H, 13C, and 18O tracers requires only 354 EMUs compared to >2,000,000 isotopomers"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000051 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000051 "http://www.ncbi.nlm.nih.gov/pubmed/17088092"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000051 "metran"@en) +SubClassOf(obo:MSIO_0000051 obo:IAO_0000010) + +# Class: obo:MSIO_0000052 (midcor) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000052 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000052 "“midcor.R” is an “R”-program that performs a primary analysis of isotopic isomers (isotopomers) distribution obtained by Gas Chromatography coupled with Mass Spectrometry (GCMS). The aim of this analysis is to have a correct distribution of isotopes originated from substrates that are artificially enriched with specific isotopes (usually 13C). To this end the program performs a correction for natural occurring isotopes and also correction for “impurities” of the assay media that give peaks overlapping with the spectra of analyzed labeled metabolites. This program offers two ways of corrections of “impurities” resulted from overlapping the assayed mass isotopomer distribution with peaks produced either by unknown metabolites in the media, or by different fragments produced by the assayed metabolite. + +The source code is available from https://github.com/seliv55/midcor") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000052 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000052 "http://portal.phenomenal-h2020.eu/app-library/midcor") +AnnotationAssertion(dc:contributor obo:MSIO_0000052 "Pedra de Atauri"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000052 "Vitaly Selivanov"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000052 "midcor"@en) +SubClassOf(obo:MSIO_0000052 obo:IAO_0000010) + +# Class: obo:MSIO_0000053 (non-stationary isotopic labeling experiment) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000053 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000053 "an isotopically non-stationary labeling experiment is a material processing used in fluxomics studies where cells cultures are grown in the presence of radiolabeled tracer compound for relatively short amount of time and samples collection before the system can reach an isotopic and metabolic steady state, and is therefore in a non-stationary phase. Such experiment are shorter to run that steady-state labeling experiment and usually allow to determine fluxes with increased precision."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000053 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000053 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000053 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000053 "non-stationary isotopic labeling experiment"@en) +SubClassOf(obo:MSIO_0000053 obo:MSIO_0000096) +SubClassOf(obo:MSIO_0000053 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) +DisjointClasses(obo:MSIO_0000053 obo:MSIO_0000185) + +# Class: obo:MSIO_0000054 (13C5-15N2-glutamine) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000054 obo:IAO_0000226) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000054 "A non-radioactive, glutamine molecule in which 5 carbons are substituted with stable carbon 13 (13C) isotope and both glutamin nitrogen atoms are substituted with 15N ones, with potential imaging application or fluxomics studies."@en) +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000054 "submit to CHEBI"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000054 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000054 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000054 "184161-19-1"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000054 "13C5-15N2-glutamine"@en) +SubClassOf(obo:MSIO_0000054 obo:CHEBI_23367) +SubClassOf(obo:MSIO_0000054 ObjectSomeValuesFrom(obo:OBI_0000312 obo:MSIO_0000120)) + +# Class: obo:MSIO_0000055 (openMoebius) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000055 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000055 "OpenMoebius is an integrated software for conventional 13C-Metabolic Flux Analysis and isotopically nonstationary 13C-Metabolic Flux Analysis (INST-13C-MFA). This work is partially supported by JST, Strategic International Collaborative Research Program, SICORP for JP-US Metabolomics. +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000055 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000055 "http://www-shimizu.ist.osaka-u.ac.jp/hp/en/software/OpenMebius.html"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000055 "openMoebius"@en) +SubClassOf(obo:MSIO_0000055 obo:IAO_0000010) + +# Class: obo:MSIO_0000056 (ramid) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000056 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000056 "RaMID is a computer program designed to read the machine-generated files saved in netCDF format containing registered time course of m/z chromatograms. It evaluates the peaks of mass isotopomer distribution (MID) making them ready for further correction for natural isotope occurrence. RaMID is written in “R”, uses library “ncdf4” (it should be installed before the first use of RaMID) and contains several functions, located in the files “ramid.R” and \"libcdf.R,\" designed to read CDF files, and analyze and visualize the spectra that they contain. + +the source code is available from: https://github.com/seliv55/RaMID") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000056 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000056 "https://github.com/seliv55/RaMID"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000056 "Pedro de Atauri"@en) +AnnotationAssertion(dc:contributor obo:MSIO_0000056 "Vitaly Selivanov"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000056 "ramid"@en) +SubClassOf(obo:MSIO_0000056 obo:IAO_0000010) + +# Class: obo:MSIO_0000057 (sumoflux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000057 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000057 "a software produced by Nicolas Zamboni and colleagues for flux ratio estimation based on a 5 step workflow known as SUMOFLUX and which relies on surrogate modeling. + +Matlab code available from: +http://www.imsb.ethz.ch/research/zamboni/resources.html"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000057 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000057 "http://ncbi.nlm.nih.gov/pubmed/27626798"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000057 "sumoflux"@en) +SubClassOf(obo:MSIO_0000057 obo:IAO_0000010) + +# Class: obo:MSIO_0000058 (network) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000058 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000058 "The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000058 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000058 "adapted from wikipedia: +https://en.wikipedia.org/wiki/Biological_network"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000058 "network"@en) +SubClassOf(obo:MSIO_0000058 obo:IAO_0000030) + +# Class: obo:MSIO_0000059 (pathway) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000059 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000059 "a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000059 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000059 "https://en.wikipedia.org/wiki/Metabolic_pathway"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000059 "pathway"@en) +SubClassOf(obo:MSIO_0000059 obo:IAO_0000030) + +# Class: obo:MSIO_0000060 (stoichiometric coefficient) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000060 "CH4 + 2 O2 → CO2 + 2 H2O, the stoichiometric coefficient of CH4 is -1, the stoichiometric coefficient of O2 is -2, for CO2 it would be +1 and for H2O it is +2"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000060 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000060 "a stoichiometric coefficient is an information object which is part of an equation describing a chemical reaction and which corresponds to the number of molecules of a reactant taking part in a reaction."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000060 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000060 "http://en.wikipedia.org/wiki/Stoichiometry#Stoichiometric_coefficient"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000060 "stoichiometric coefficient"@en) +SubClassOf(obo:MSIO_0000060 obo:IAO_0000030) +SubClassOf(obo:MSIO_0000060 ObjectSomeValuesFrom(obo:IAO_0000219 obo:MSIO_0000001)) + +# Class: obo:MSIO_0000061 (cell culture doubling time) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000061 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000061 "the amount of time elapsed for a cell culture to growth twice its initial size, usually expressed in hour"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000061 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000061 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000061 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000061 "cell culture doubling time"@en) +SubClassOf(obo:MSIO_0000061 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000061 ObjectSomeValuesFrom(obo:IAO_0000039 ObjectUnionOf(obo:UO_0000010 obo:UO_0000031))) +SubClassOf(obo:MSIO_0000061 ObjectSomeValuesFrom(obo:IAO_0000136 obo:OBI_0100060)) + +# Class: obo:MSIO_0000062 (cell seeding density) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000062 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000062 "Cell seeding density is a measurement datum which denotes the number of cells per surface area in the case of adherent cells or number of cells per volume in the case of free cells deposited in the culture vessel to start a cell culture. The cell seeding density is therefore stated in number of cells per cm2 or number of cells per ml."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000062 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000062 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000062 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000062 "cell seeding density"@en) +SubClassOf(obo:MSIO_0000062 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000062 ObjectSomeValuesFrom(obo:IAO_0000136 obo:OBI_0100060)) + +# Class: obo:MSIO_0000063 (cell volume) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000063 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000063 "average cell volume is a measurement datum used to report over physcal occupancy of cells under study. This information is used for as input for kinetic modeling."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000063 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000063 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000063 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000063 "cell volume"@en) +SubClassOf(obo:MSIO_0000063 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000063 ObjectSomeValuesFrom(obo:IAO_0000219 obo:CL_0000010)) + +# Class: obo:MSIO_0000064 (confluence level) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000064 "when cells reach 50% confluence level, replenish medium"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000064 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000064 "confluence level is a measurement datum denotes the status of a cell culture and how cells are occupying the space available in a plate. confluence levels are stated in %."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000064 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000064 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000064 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000064 "confluence level"@en) +SubClassOf(obo:MSIO_0000064 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000064 ObjectSomeValuesFrom(obo:IAO_0000136 obo:OBI_0100060)) + +# Class: obo:MSIO_0000065 (dilution factor) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000065 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000065 "dilution factor is a measurement data item which indicates in percentage the level of purity of a material in the context of dilution such as a dilution series."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000065 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000065 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000065 "dilution factor"@en) +SubClassOf(obo:MSIO_0000065 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000065 ObjectSomeValuesFrom(obo:IAO_0000136 obo:MSIO_0000016)) + +# Class: obo:MSIO_0000066 (DNA content) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000066 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000066 "the amount of dideoxyribonucleic acids present in a cell culture or tissue. +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000066 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000066 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000066 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000066 "DNA content"@en) +SubClassOf(obo:MSIO_0000066 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000066 ObjectSomeValuesFrom(obo:IAO_0000219 obo:CL_0000010)) + +# Class: obo:MSIO_0000067 (interacellular metabolite average content) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000067 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000067 "intracellular metabolite average content is a measurement provided of metabolite concentration normalized against cell average volume or DNA content or protein content or dry weight"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000067 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000067 "metabolite content"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000067 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000067 "cosmos tracer based metabolomics working group +Barcelona meeting, march 2015"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000067 "interacellular metabolite average content"@en) +SubClassOf(obo:MSIO_0000067 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000067 ObjectSomeValuesFrom(obo:IAO_0000219 obo:CL_0000010)) + +# Class: obo:MSIO_0000069 (metabolite concentration) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000069 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000069 "the concentration of a molecular entity acting as metabolite and stated in standard concentration units, such molar, micromolar and so on"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000069 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000069 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000069 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000069 "metabolite concentration"@en) +SubClassOf(obo:MSIO_0000069 obo:IAO_0000109) + +# Class: obo:MSIO_0000070 (metabolite pool size estimate) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000070 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000070 "metabolite pool size estimate is an information entity used in fluxomics studies to estimate the amount of molecular entity available to a particular metabolic process. It is usually reported in umol per mg of protein."@en) +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000070 "can be also computed from simulation and be output of such simulation (then provide confidence indicator) +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000070 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000070 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000070 "pool size"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000070 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000070 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000070 "metabolite pool size estimate"@en) +SubClassOf(obo:MSIO_0000070 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000070 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectUnionOf(obo:MSIO_0000059 ObjectSomeValuesFrom(obo:RO_0000087 obo:CHEBI_25212)))) + +# Class: obo:MSIO_0000071 (passage number) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000071 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000071 "passage number is a measurement data item denoting how many times a cell culture has been split and transferred to a new culture vessel. It can also be considered to be equivalent to how many times a cell culture has reached 100% confluence"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000071 "Philippe Rocca-Serra +"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000071 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000071 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000071 "passage number"@en) +SubClassOf(obo:MSIO_0000071 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000071 ObjectSomeValuesFrom(obo:IAO_0000136 obo:OBI_0100060)) + +# Class: obo:MSIO_0000072 (protein concentration) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000072 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000072 "ratio of protein content over a reference standard element (usually bovine serum albumin (BSA))"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000072 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000072 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000072 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000072 "protein concentration"@en) +SubClassOf(obo:MSIO_0000072 obo:IAO_0000109) + +# Class: obo:MSIO_0000073 (protein content) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000073 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000073 "the amount of (soluble) protein from cell culture or tissue. the quantity of total protein recovered from an extraction process varies depending on the solvent and buffers used during the extraction phase. the amount is usuall expressed in milligram (refer to Unit Ontology)"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000073 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000073 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000073 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000073 "protein content"@en) +SubClassOf(obo:MSIO_0000073 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000073 ObjectSomeValuesFrom(obo:BFO_0000051 obo:IAO_0000414)) +SubClassOf(obo:MSIO_0000073 ObjectSomeValuesFrom(obo:IAO_0000219 obo:CL_0000010)) + +# Class: obo:MSIO_0000074 (signal intensity) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000074 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000074 "signal intensity is a kind of measurement providing an estimate of the strength of a phenomena as it is recorded. For digital detector instrument, the signal intensity is usually a electric intensity or a field strength of the electromagnetic wave transmitting a signal.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000074 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000074 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000074 "cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000074 "signal intensity"@en) +SubClassOf(obo:MSIO_0000074 obo:IAO_0000109) + +# Class: obo:MSIO_0000075 (maximum m/z values signal intensity with baseline substraction) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000075 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000075 "Signal intensity of all m/z values at the maximum of the peak (also known as maximum signal intensity) and subtracting baseline."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000075 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000075 "peak height as signal intensity"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000075 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000075 "cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000075 "maximum m/z values signal intensity with baseline substraction"@en) +SubClassOf(obo:MSIO_0000075 obo:MSIO_0000074) + +# Class: obo:MSIO_0000076 (total volume of cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000076 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000076 "total volume of cell culture is a measurement data item which denotes the volume occupied by a cell culture"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000076 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000076 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000076 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000076 "total volume of cell culture"@en) +SubClassOf(obo:MSIO_0000076 obo:IAO_0000109) + +# Class: obo:MSIO_0000077 (isotopologue distribution matrix) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000077 "https://github.com/ISA-tools/isa-matrix-datapackages/tree/master/src/sirm_datapkg") +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000077 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000077 "an isotopologue distribution matrix is an information object used in tracer based metabolomics experiments to report the amount of possible isotopologues (sets of isotopomers) derived from the tracer in a metabolic network. + +the matrix hold the mass isotopomer distributions (MIDs) of Elementary Metabolite Unit (EMU) which will be used as state variables. An EMU is defined as a distinct subset of a metabolite’s atoms. EMUs can exist in a variety of mass states depending on their isotopic compositions. An EMU in its lowest mass state is referred to as M+0, while an EMU that contains one additional atomic mass unit (e.g., due to the presence of a 13C atom in place of a 12C atom) is referred to as M+1, with higher mass states described accordingly. An MID is a vector that contains the fractional abundance of each mass state of an EMU."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000077 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000077 "DOI 10.1002/bit.21632 +An Elementary Metabolite Unit (EMU) BasedMethod of Isotopically Nonstationary Flux Analysis, +Jamey D. Young, Jason L. Walther, Maciek R. Antoniewicz, Hyuntae Yoo,Gregory Stephanopoulos, Department of Chemical Engineering, Massachusetts Institute of Technology. +http://onlinelibrary.wiley.com/doi/10.1002/bit.21632/epdf"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000077 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000077 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000077 "isotopologue distribution matrix"@en) +SubClassOf(obo:MSIO_0000077 obo:IAO_0000306) +SubClassOf(obo:MSIO_0000077 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf( obo:MSIO_0000074 obo:MSIO_0000187 obo:MSIO_0000190 obo:MSIO_0000194))) + +# Class: obo:MSIO_0000078 (metabolic flux rate matrix) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000078 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000078 "a metabolic flux rate matrix is an information content entity which is defined as a 2 dimensional table associating chemical species with uptake and excretion rate in the cell") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000078 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000078 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000078 "cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000078 "metabolic flux rate matrix"@en) +SubClassOf(obo:MSIO_0000078 obo:IAO_0000306) + +# Class: obo:MSIO_0000079 (stoichiometry matrix) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000079 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000079 "a stoichiometry matrix is an information content entity holding arrays of stoichiometric coefficients, each associated to a specific chemical reactions"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000079 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000079 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000079 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000079 "stoichiometry matrix"@en) +SubClassOf(obo:MSIO_0000079 obo:IAO_0000306) +SubClassOf(obo:MSIO_0000079 ObjectSomeValuesFrom(obo:BFO_0000051 obo:MSIO_0000060)) +SubClassOf(obo:MSIO_0000079 ObjectMinCardinality(1 obo:IAO_0000136 obo:MSIO_0000001)) + +# Class: obo:MSIO_0000080 (metabolite identifier) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000080 "a CHEBI identifier for chemical or an HMDB identifier"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000080 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000080 "a centrally registered identifier to denote a metabolite chemical entity"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000080 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000080 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000080 "metabolite identifier"@en) +SubClassOf(obo:MSIO_0000080 obo:IAO_0000578) + +# Class: obo:MSIO_0000081 (pathway identifier) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000081 "a KEGG pathway identifier such as map00010 (http://www.genome.jp/dbget-bin/www_bget?map00010)"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000081 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000081 "a centrally registered identifier which denotes a pathway data item"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000081 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000081 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000081 "pathway identifier"@en) +SubClassOf(obo:MSIO_0000081 obo:IAO_0000578) + +# Class: obo:MSIO_0000082 (protein identifier) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000082 "a uniprot identifier such P20248 (http://www.uniprot.org/uniprot/P20248)"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000082 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000082 "a centrally registered identifier to denote a molecular entity of the type Protein."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000082 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000082 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000082 "protein identifier"@en) +SubClassOf(obo:MSIO_0000082 obo:IAO_0000578) + +# Class: obo:MSIO_0000083 (reaction identifier) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000083 "a reactome identifier such as R-HSA-174054"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000083 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000083 "a centrally registered identifier which denotes a chemical reaction."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000083 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000083 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000083 "reaction identifier"@en) +SubClassOf(obo:MSIO_0000083 obo:IAO_0000578) + +# Class: obo:MSIO_0000084 (calibration) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000084 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000084 "calibration is a process which relies on comparison between measurements in order to estimate the reliability of the measurements performed on a particular device or instrument configuration. +a calibration process may be used to identify a systematic error in measurement and possibly include it into an error model. +a calibration process may be used to detect degradation of parts of instruments when long data acquisition times are needed (e.g. degradation of a chromatography column in a GC-MS chain). + +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000084 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000084 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000084 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000084 "calibration"@en) +SubClassOf(obo:MSIO_0000084 obo:OBI_0000011) + +# Class: obo:MSIO_0000085 (quality control) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000085 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000085 "quality control is a process which aims to ensure that procedures for producing a material or a measurement remain within established error tolerance margins. Quality control often relies on the use of references or standards against which readings are gauged. those standards can be 'negative control' which should produce in an absence of signal or 'positive control', which should result in the presence of a signal of known quality and intensity."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000085 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000085 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000085 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000085 "quality control"@en) +SubClassOf(obo:MSIO_0000085 obo:OBI_0000011) + +# Class: obo:MSIO_0000086 (assessing across studies variability) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000086 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000086 "assessing across studies variability is a quality control process which aims at monitoring the consistency of signal acquisitions between different studies (for instance in the context of meta-analysis and data integration) in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000086 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000086 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000086 "assessing across studies variability"@en) +SubClassOf(obo:MSIO_0000086 obo:MSIO_0000085) + +# Class: obo:MSIO_0000087 (assessing instrument conditioning) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000087 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000087 "assessing instrument conditionning is a quality control process which aims at monitoring the stability of the analytical instrument prior to running data acquisition on specimen of interest by running a set of control runs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000087 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000087 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000087 "assessing instrument conditioning"@en) +SubClassOf(obo:MSIO_0000087 obo:MSIO_0000085) + +# Class: obo:MSIO_0000088 (assessing within study variability) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000088 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000088 "assessing within study variability is a quality control process which aims at monitoring the consistency of signal acquisition throughout the course of a study in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000088 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000088 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000088 "assessing within study variability"@en) +SubClassOf(obo:MSIO_0000088 obo:MSIO_0000085) + +# Class: obo:MSIO_0000089 (assessing study batch to batch variation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000089 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000089 "assessing study batch-to-batch variation is a within study variably quality control which specifically looks at how batching of data acquisition contributes to adding unwanted noice and how to account for it."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000089 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000089 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000089 "assessing study batch to batch variation"@en) +SubClassOf(obo:MSIO_0000089 obo:MSIO_0000088) + +# Class: obo:MSIO_0000090 (detecting carry over event) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000090 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000090 "detecting carry over event is a quality control process which aims to determine if measurements in one sample are affected to earlier measurements made on different samples and indicative of insufficient matrix regeneration between 2 data acquisition events. this is usually assessed by running solvent blanks or sample preparation blank between analytical runs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000090 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000090 "carry over detection"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000090 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000090 "detecting carry over event"@en) +SubClassOf(obo:MSIO_0000090 obo:MSIO_0000085) +SubClassOf(obo:MSIO_0000090 ObjectSomeValuesFrom(obo:RO_0000057 ObjectUnionOf(obo:MSIO_0000025 obo:MSIO_0000026))) + +# Class: obo:MSIO_0000091 (detecting departure from linearity event) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000091 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000091 "detecting departure from linearity event is a quality control process which aims to determine if measurements respond in a linear fashion of a linear increase of concentration of analytes. this is usually assessed by running a dilution series between analytical runs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000091 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000091 "linearity departure detection"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000091 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000091 "detecting departure from linearity event"@en) +SubClassOf(obo:MSIO_0000091 obo:MSIO_0000085) +SubClassOf(obo:MSIO_0000091 ObjectSomeValuesFrom(obo:RO_0000057 obo:MSIO_0000016)) + +# Class: obo:MSIO_0000092 (detecting sample degradation event) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000092 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000092 "detecting sample degradation event is a quality control process which aims to determine if measurements in samples are affected by their run order or time of acquisition. This is usually assessed by running the same analytical samples at different points along the data acquistion plan (technical replication at the begining and end of runs)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000092 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000092 "sample degradatation detection"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000092 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000092 "detecting sample degradation event"@en) +SubClassOf(obo:MSIO_0000092 obo:MSIO_0000085) +SubClassOf(obo:MSIO_0000092 ObjectSomeValuesFrom(obo:RO_0000057 obo:MSIO_0000025)) + +# Class: obo:MSIO_0000094 (metabolomics investigation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000094 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000094 "an investigation which focused on measuring small biological molecules known as metabolite with the goal of understanding biochemical process underlying normal or pathological biological processes"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000094 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000094 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000094 "metabolomics investigation"@en) +EquivalentClasses(obo:MSIO_0000094 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectUnionOf(obo:MSIO_0000100 obo:MSIO_0000101))) +SubClassOf(obo:MSIO_0000094 obo:OBI_0000066) + +# Class: obo:MSIO_0000095 (lipidomics investigation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000095 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000095 "lipidomics investigation is an investigation which aims at determining the lipid content of a biological system under given experimental conditions using data acquisition techniques such as mass spectrometry, nmr spectroscopy or chromatography techniques."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000095 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000095 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000095 "lipidomics investigation"@en) +SubClassOf(obo:MSIO_0000095 ObjectIntersectionOf(obo:MSIO_0000094 ObjectSomeValuesFrom(obo:OBI_0000293 obo:CHEBI_18059))) + +# Class: obo:MSIO_0000096 (stable isotope resolved metabolomics study) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000096 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000096 "stable isotope resolved metabolomics study is a kind of investigation which uses non-radioactive isotope for labeling compounds which are precursors in key metabolic reaction. These studies therefore allow deciphering reaction and understanding the fluxes in cells. +Tracer based pathway discovery study is a specific type of fluxomics study which aims at discovery new metabolic routes and their associated signature metabolites by using isotopically labeled tracers"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000096 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000096 "SIRMS") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000096 "tracer based metabolite profiling"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000096 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000096 "stable isotope resolved metabolomics study") +SubClassOf(obo:MSIO_0000096 obo:MSIO_0000134) +SubClassOf(obo:MSIO_0000096 ObjectSomeValuesFrom(obo:BFO_0000051 obo:MSIO_0000130)) +SubClassOf(obo:MSIO_0000096 ObjectSomeValuesFrom(obo:BFO_0000051 obo:MSIO_0000131)) +SubClassOf(obo:MSIO_0000096 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectUnionOf(obo:MSIO_0000053 obo:MSIO_0000185))) + +# Class: obo:MSIO_0000099 (metabolite quantitation using high performance liquid chromatography) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000099 "A kind of assay which attempts to identify and measure relative concentration of all possible metabolites using the method high-performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography), is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000099 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000099 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000099 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000099 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000099 "https://en.wikipedia.org/wiki/High-performance_liquid_chromatography"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000099 "metabolite quantitation using high performance liquid chromatography"@en) +SubClassOf(obo:MSIO_0000099 obo:OBI_0000070) + +# Class: obo:MSIO_0000100 (targeted metabolite profiling) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000100 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000100 "a kind of assay which attempts to identify and measure specific compound/ metabolites (known in advance) expressed as concentration or relative abundance ratio to a standard in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy or liquid chromatography DAD"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000100 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000100 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000100 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000100 "targeted metabolite profiling"@en) +SubClassOf(obo:MSIO_0000100 obo:OBI_0000070) + +# Class: obo:MSIO_0000101 (untargeted metabolite profiling) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000101 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000101 "a kind of assay which attempts to identify and measure relative concentration of all possible metabolites present in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000101 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000101 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000101 "global metabolite profiling") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000101 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000101 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000101 "untargeted metabolite profiling"@en) +SubClassOf(obo:MSIO_0000101 obo:OBI_0000070) + +# Class: obo:MSIO_0000102 (fresh culture medium) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000102 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000102 "a fresh culture medium is a culture medium which presents its nominal characteristisc in terms of molecular concentration of its components, pH, and physical chemical expected properties."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000102 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000102 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000102 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000102 "fresh culture medium"@en) +SubClassOf(obo:MSIO_0000102 obo:OBI_0000079) + +# Class: obo:MSIO_0000103 (spent culture medium) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000103 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000103 "spent culture medium is a culture medium which has been added to a cell culture and which has been depleted of its component as used by the growing cell and which has received the by products of cell metabolites excreted by the cells. Therefore, spent culture medium will different significantly in pH and physical chemical properties from the initial fresh culture medium added to the cell as the begining of the cell culture. Spent culture medium is usually recovered by aspiration or mild centrifugation (as not to distrupt cell membrane) of the cell culture."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000103 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000103 "cell culture supernatant"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000103 "spent medium"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000103 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000103 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000103 "spent culture medium"@en) +SubClassOf(obo:MSIO_0000103 obo:OBI_0000079) + +# Class: obo:MSIO_0000104 (metabolism quenching) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000104 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000104 "metabolism quenching is a planned processed whose objective is a quick extinction of all biochemical reactions occuring in a biological system in order to fix molecular entity concentrations for downstream quantitation and analysis. An array of physical or chemical agent may be used to achieve that goal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000104 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000104 "metabolism immediate extinction"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000104 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000104 "metabolism quenching"@en) +SubClassOf(obo:MSIO_0000104 obo:OBI_0000094) + +# Class: obo:MSIO_0000105 (direct metabolism quenching by solvent) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000105 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000105 "direct metabolism quenching by solvent is a kind biochemical reaction extinction process which relies on organic solvents to denature enzymatic machinery and inactivate it."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000105 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000105 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000105 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000105 "direct metabolism quenching by solvent"@en) +SubClassOf(obo:MSIO_0000105 obo:MSIO_0000104) + +# Class: obo:MSIO_0000106 (metabolism quenching by 13 CD3-QDA in cold CH3CN) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000106 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000106 "a type of metabolism immediate extinction using cold acetonitrile"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000106 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000106 "metabolism quenching using QDA"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000106 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000106 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000106 "metabolism quenching by 13 CD3-QDA in cold CH3CN"@en) +SubClassOf(obo:MSIO_0000106 obo:MSIO_0000105) + +# Class: obo:MSIO_0000107 (metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000107 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000107 "a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol ammonium bicarbonate solution"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000107 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000107 "cooled 60% methanol NH4HCO3 metabolism quenching"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000107 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000107 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000107 "metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer") +SubClassOf(obo:MSIO_0000107 obo:MSIO_0000104) + +# Class: obo:MSIO_0000108 (metabolism quenching using precooled 60 percent methanol HEPES buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000108 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000108 "a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol HEPES solution"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000108 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000108 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000108 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000108 "metabolism quenching using precooled 60 percent methanol HEPES buffer") +SubClassOf(obo:MSIO_0000108 obo:MSIO_0000104) + +# Class: obo:MSIO_0000109 (metabolism quenching using precooled PBS buffer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000109 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000109 "a type of metabolism extinction which uses refrigerated PBS buffer"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000109 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000109 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000109 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000109 "metabolism quenching using precooled PBS buffer") +SubClassOf(obo:MSIO_0000109 obo:MSIO_0000104) + +# Class: obo:MSIO_0000110 (elution program) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000110 "acetonitrile 5%, isopropanol 95% for 15 minutes at flow rate 1 ml/min,"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000110 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000110 "an elution program is a set of recorded instructions which determine the mobile phase (gas or liquid) composition, pressure, temperature and flow rate during the chromatography separation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000110 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000110 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000110 "elution program"@en) +SubClassOf(obo:MSIO_0000110 obo:OBI_0000272) + +# Class: obo:MSIO_0000111 (derivatization) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000111 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000111 "derivatization is a technique used in chemistry which transforms a chemical compound into a product (the reaction's derivate) of similar chemical structure, called a derivative. That compound has properties more +amenable to a particular analytical method. Some samples analyzed by GC require derivatization in order to make them suitable for analysis. Compounds that have poor volatility, poor thermal stability, or that can be adsorbed in the injector will exhibit nonreproducible peak areas, heights, and shapes. Other compounds that respond poorly on a specific detector may need to be “tagged” with a different functional group to improve detection.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000111 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000111 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000111 "adapted from https://en.wikipedia.org/wiki/Derivatization and https://www.restek.com/pdfs/CFTS1269.pdf. +Last accessed: 2018-01-11") +AnnotationAssertion(rdfs:label obo:MSIO_0000111 "derivatization"@en) +EquivalentClasses(obo:MSIO_0000111 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000029)) +SubClassOf(obo:MSIO_0000111 obo:OBI_0000652) + +# Class: obo:MSIO_0000112 (acetylation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000112 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000112 "a kind of derivatization which results in the addition of acetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000112 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000112 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000112 "EU cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000112 "acetylation"@en) +SubClassOf(obo:MSIO_0000112 obo:MSIO_0000111) + +# Class: obo:MSIO_0000113 (trifluoroacetylation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000113 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000113 "a kind of derivatization which results in the addition of trifluoroacetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000113 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000113 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000113 "EU H2020 PhenoMenal") +AnnotationAssertion(rdfs:label obo:MSIO_0000113 "trifluoroacetylation"@en) +SubClassOf(obo:MSIO_0000113 obo:MSIO_0000112) + +# Class: obo:MSIO_0000114 (alkylation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000114 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000114 "a kind of derivatization which results in the addition of alkyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000114 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000114 "EU H2020 PhenoMenal") +AnnotationAssertion(rdfs:label obo:MSIO_0000114 "alkylation"@en) +SubClassOf(obo:MSIO_0000114 obo:MSIO_0000111) + +# Class: obo:MSIO_0000115 (methylation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000115 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000115 "a kind of derivatization which results in the addition of methyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000115 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000115 "EU H2020 PhenoMenal") +AnnotationAssertion(rdfs:label obo:MSIO_0000115 "methylation"@en) +SubClassOf(obo:MSIO_0000115 obo:MSIO_0000111) + +# Class: obo:MSIO_0000116 (oximation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000116 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000116 "a kind of derivatization which results in the addition of oxime group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000116 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000116 "EU H2020 PhenoMenal") +AnnotationAssertion(rdfs:label obo:MSIO_0000116 "oximation"@en) +SubClassOf(obo:MSIO_0000116 obo:MSIO_0000111) + +# Class: obo:MSIO_0000117 (silylation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000117 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000117 "a kind of derivatization which results in the addition of silyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000117 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000117 "EU H2020 PhenoMenal") +AnnotationAssertion(rdfs:label obo:MSIO_0000117 "silylation"@en) +SubClassOf(obo:MSIO_0000117 obo:MSIO_0000111) + +# Class: obo:MSIO_0000118 (isotopic labeling) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000118 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000118 "Isotopic labeling (or isotopic labelling) is a technique used to track the passage of an isotope (an atom with a detectable variation) through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000118 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000118 "https://en.wikipedia.org/wiki/Isotopic_labeling"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000118 "isotopic labeling"@en) +SubClassOf(obo:MSIO_0000118 obo:OBI_0000652) + +# Class: obo:MSIO_0000119 (isotopic labeling with positional labeled tracer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000119 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000119 "Specific isotopic labeling refers to the placement of a single label (e.g., 2H, 13C, or 15N) in a specified location in a molecule."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000119 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000119 "specific isotopic labeling"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000119 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000119 "http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000119 "isotopic labeling with positional labeled tracer"@en) +SubClassOf(obo:MSIO_0000119 obo:MSIO_0000118) +SubClassOf(obo:MSIO_0000119 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) +SubClassOf(obo:MSIO_0000119 ObjectSomeValuesFrom(obo:OBI_0000299 obo:MSIO_0000032)) + +# Class: obo:MSIO_0000120 (isotopic labeling with uniformly labeled tracer) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000120 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000120 "Uniform labeling refers to biosynthetic labeling of all carbon, nitrogen, or hydrogen sites with stable isotopes. Uniform labeling of proteins with 15N is particularly convenient because of the strategic locations of nitrogens in the backbone and the absence of homonuclear couplings due to the intervening carbons. It is also possible to replace all of the carbons with 13C, although in this case the spectroscopy has to deal with the network of couplings among bonded carbons. Similarly, all of the hydrogens can be replaced with deuterons in order to attenuate the dipolar couplings among the hydrogens that often present complications and difficulties in the experiments."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000120 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000120 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000120 "http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000120 "isotopic labeling with uniformly labeled tracer"@en) +SubClassOf(obo:MSIO_0000120 obo:MSIO_0000118) +SubClassOf(obo:MSIO_0000120 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) +SubClassOf(obo:MSIO_0000120 ObjectSomeValuesFrom(obo:OBI_0000299 obo:MSIO_0000033)) + +# Class: obo:MSIO_0000121 (collection at cell cycle phase) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000121 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000121 "a process of collecting a sample when the cells of cell culture growth are collected at a specific phase of the cell division cycle (e.g collection at G2/G1). This often requires a cell synchronization step."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000121 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000121 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000121 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000121 "collection at cell cycle phase"@en) +SubClassOf(obo:MSIO_0000121 obo:OBI_0000659) + +# Class: obo:MSIO_0000122 (collection at cytostatic phase) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000122 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000122 "a process of collecting a sample when the cells of a cell culture growth are not dividing"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000122 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000122 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000122 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000122 "collection at cytostatic phase"@en) +SubClassOf(obo:MSIO_0000122 obo:OBI_0000659) + +# Class: obo:MSIO_0000123 (collection at logarithmic phase) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000123 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000123 "a process of collecting a sample when the cell culture growth can be approximated by a logarithm function."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000123 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000123 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000123 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000123 "collection at logarithmic phase") +SubClassOf(obo:MSIO_0000123 obo:OBI_0000659) + +# Class: obo:MSIO_0000124 (collection at specific cell culture passage) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000124 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000124 "collection at specific cell culture passage is a kind of specimen collection which occurs after a strictly defined number of cell culture splitting, defined to control how many cell divisions have been performed."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000124 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000124 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000124 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000124 "collection at specific cell culture passage"@en) +SubClassOf(obo:MSIO_0000124 obo:OBI_0000659) + +# Class: obo:MSIO_0000125 (collection at stabilization phase before experiment) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000125 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000125 "collection at stabilization phase before experiment is a kind of specimen collection process which takes places once cells have reached a stationary growth phase and prior the main experimental intervention is applied."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000125 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000125 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000125 "cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000125 "collection at stabilization phase before experiment"@en) +SubClassOf(obo:MSIO_0000125 obo:OBI_0000659) + +# Class: obo:MSIO_0000126 (collection at stationary phase) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000126 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000126 "a process of collecting a sample when the cell culture growth has reached a plateau, indicative of a steady state"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000126 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000126 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000126 "collection at steady state phase"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000126 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000126 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000126 "collection at stationary phase"@en) +SubClassOf(obo:MSIO_0000126 obo:OBI_0000659) + +# Class: obo:MSIO_0000127 (flux balance analysis) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000127 "") +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000127 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000127 "Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. Flux balance analysis calculates the flow of metabolites through a metabolic network, thereby making it possible to predict the growth rate of an organism or the rate of production of a biotechnologically important metabolite.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000127 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000127 "What is flux balance analysis? +Jeffrey D. Orth, Ines Thiele, and Bernhard Ø. Palsson + +Nat Biotechnol. 2010 Mar; 28(3): 245–248. +doi: 10.1038/nbt.1614") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000127 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000127 "flux balance analysis"@en) +SubClassOf(obo:MSIO_0000127 obo:OBI_0200000) +SubClassOf(obo:MSIO_0000127 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectUnionOf(obo:MSIO_0000077 obo:MSIO_0000078))) + +# Class: obo:MSIO_0000128 (13C-constrained flux balance analysis) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000128 "") +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000128 "") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000128 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000128 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000128 "13C-constrained flux balance analysis"@en) +SubClassOf(obo:MSIO_0000128 obo:MSIO_0000127) + +# Class: obo:MSIO_0000129 (isotopomer data matrix) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000129 "an isotopomer data matrix is a table resulting from the analysis of NMR data acquired in the context of tracer based studies and which contains information about chemical entity assignment") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000129 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000129 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000129 "isotopomer data matrix") +SubClassOf(obo:MSIO_0000129 obo:IAO_0000306) +SubClassOf(obo:MSIO_0000129 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf( obo:IAO_0000578 obo:MSIO_0000191 obo:MSIO_0000194))) + +# Class: obo:MSIO_0000130 (isotope natural abundance correction) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000130 "Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. +BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139.") +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000130 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000130 "natural abundance correction is a data transformation which aims to take into account the contribution of natural random variation in isotopic composition in the environment and adjust for it during the calculation of mass isotopologue distribution in a tracer based metabolomics experiment"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000130 "Hunter Moseley") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000130 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000130 "BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139. +Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry."@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000130 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000130 "isotope natural abundance correction"@en) +SubClassOf(obo:MSIO_0000130 obo:OBI_0200000) +SubClassOf(obo:MSIO_0000130 ObjectSomeValuesFrom(obo:BFO_0000050 obo:MSIO_0000096)) + +# Class: obo:MSIO_0000131 (metabolic flux analysis) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000131 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000131 "metabolic flux analysis is a type of investigation which uses data from tracer based studies to provide insights into cellular metabolites creation and destruction."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000131 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000131 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000131 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000131 "metabolic flux analysis"@en) +SubClassOf(obo:MSIO_0000131 obo:MSIO_0000134) +SubClassOf(obo:MSIO_0000131 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) + +# Class: obo:MSIO_0000132 (steady state 13C metabolic flux analysis) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000132 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000132 "steady-state 13C metabolic flux analysis is a metabolic flux analysis approach which relies on 13C tracer experiments and requires long incubation period necessary to meet methodological requirements that all reactions under study have reach steady state. + +By feeding cells a 13C-labeled substrate and subsequently measuring the patterns of isotope incorporation in downstream metabolic products, extensive information about the intracellular distribution of carbon flux can be obtained. This enables system-wide quantification of reversible, parallel, and cyclic metabolic pathways that would be otherwise unidentifiable based solely upon measurements of extracellular nutrient uptake and product excretion (Zamboni et al., 2009). + +While 13C MFA provides a rich source of phenotypic information, the application of this technique to mammalian systems presents unique challenges. In particular, the presence of subcellular compartmentation, complex media formulations, and slow labeling dynamics can lead to significant difficulties in experimental design and data interpretation (Zamboni, 2011)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000132 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000132 "conventional 13C metabolic flux analysis"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000132 "conventional 13C-MFA"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000132 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000132 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000132 "https://www.ncbi.nlm.nih.gov/pubmed/22140245"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000132 "steady state 13C metabolic flux analysis"@en) +SubClassOf(obo:MSIO_0000132 obo:MSIO_0000131) + +# Class: obo:MSIO_0000133 (isotopically non-stationary 13C-metabolic flux analysis) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000133 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000133 "Isotopically non-stationary MFA (INST-MFA) is a metabolic flux analysis which provides an approach to circumvent limitations from other methods through computational analysis of metabolite labeling patterns obtained during the transient labeling period prior to isotopic steady state (Wiechert and Noh, 2005). This approach offers several advantages over steady-state MFA, including shorter experimental times and the ability to determine fluxes with increased precision (Nöh and Wiechert, 2011; Young and Walther, 2008)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000133 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000133 "INST-13C-MFA"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000133 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000133 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000133 "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535509/"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000133 "isotopically non-stationary 13C-metabolic flux analysis"@en) +SubClassOf(obo:MSIO_0000133 obo:MSIO_0000131) + +# Class: obo:MSIO_0000134 (tracer analysis) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000134 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000134 "a tracer analysis is a type of experimental procedure which relies on tracer molecules, usually non radioactive, to probe metabolic pathways and biochemical routes"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000134 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000134 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000134 "tracer analysis"@en) +SubClassOf(obo:MSIO_0000134 obo:MSIO_0000182) +SubClassOf(obo:MSIO_0000134 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) + +# Class: obo:MSIO_0000135 (normalization by optimal selection with multiple internal standards) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000135 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000135 "a normalization process which relies on the signal intensity measured for several reference compounds (internal standards) injected or added to the test samples in known quantities, thereby allowing sample comparison which have been placed on equal footing."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000135 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000135 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000135 "normalization by optimal selection with multiple internal standards"@en) +SubClassOf(obo:MSIO_0000135 obo:OBI_0200169) + +# Class: obo:MSIO_0000136 (normalization to a total sum) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000136 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000136 "a normalization process which relies on the computing to total signal intensity by simply summing up those signals and then for each sample measurements, dividing it by the total signal. The total sum is used as reference to which sample signals are then compared."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000136 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000136 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000136 "normalization to a total sum"@en) +SubClassOf(obo:MSIO_0000136 obo:OBI_0200169) + +# Class: obo:MSIO_0000137 (normalization to multiple standard with cross contribution compensation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000137 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000137 "a normalization process used in mass spectrometry signal processing which takes into account the fact that analytes can interact with internal standards and impair accurate estimatation of these. The interaction phenomenon is known as cross contribution and needs to be compensated for."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000137 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000137 "Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data. +Henning Redestig, Atsushi Fukushima, Hans Stenlund, Thomas Moritz, Masanori Arita, Kazuki Saito and Miyako Kusano. +RIKEN Plant Science Center, Tsurumi-ku, Suehiro-cho, 1-7-22 Yokohama, Kanagawa, 230-0045, Japan, and Umea Plant Science Center, Umea University, 901 87 Umea, Sweden. +Anal. Chem., 2009, 81 (19), pp 7974–7980 +DOI: 10.1021/ac901143w"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000137 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000137 "normalization to multiple standard with cross contribution compensation"@en) +SubClassOf(obo:MSIO_0000137 obo:OBI_0200169) + +# Class: obo:MSIO_0000138 (remove unwanted variation 2-step normalization) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000138 "ruv_starter_analysis(Y,X,ctl) + +http://www-personal.umich.edu/~johanngb/ruv/howto/howto.html"@en) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000138 "the 2 step normalization is a normalization process which uses 2 complementary steps provided suitable quality controls have been supplied. The process attempts to remove overall unwanted variation given suitable controls and uses factors of interest in the normalization. It relies on linear mixed effects model which utilizes quality control metabolites to obtain normalized data in typical metabolomics experiments."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000138 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000138 "RUV"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000138 "RUV-2"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000138 "Statistical Methods for Handling Unwanted Variation in Metabolomics Data. +Alysha M. De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A. Gagnon-Bartsch, Sandra Castillo, Julie A. Simpson, and Terence P. Speed +Biostatistics Unit, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC 3800, Australia +Zora Biosciences Oy, FIN-02150 Espoo, Finland +VTT Technical Research Centre of Finland, P. O. Box 1000, FI-02044 VTT Espoo, Finland +Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France +Department of Statistics, University of California, Berkeley, California United States, 94720 +Bioinformatics Division, Walter and Eliza Hall Institute, 1 G Royal Parade, Parkville, Victoria 3052, Australia +Department of Mathematics and Statistics, University of Melbourne, VIC 3800, Melbourne, Australia +Anal. Chem., 2015, 87 (7), pp 3606–3615 +DOI: 10.1021/ac502439y"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000138 "Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch and +Speed, 2012. Available at: http://biostatistics.oxfordjournals.org/content/13/3/539.full. + +Removing Unwanted Variation from High Dimensional Data with Negative Controls. GagnonBartsch, +Jacob, and Speed, 2013. Available at: http://statistics.berkeley.edu/tech-reports/820."@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000138 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000138 "http://www-personal.umich.edu/~johanngb/ruv/index.html"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000138 "remove unwanted variation 2-step normalization"@en) +SubClassOf(obo:MSIO_0000138 obo:OBI_0200169) + +# Class: obo:MSIO_0000140 (normalization to a single internal standard) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000140 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000140 "a normalization process which relies on the signal intensity measured for one reference compound (an internal standard) injected or added to the test samples in known quantity, thereby allowing sample comparison which have been placed on equal footing based on this reference."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000140 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000140 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000140 "normalization to a single internal standard"@en) +SubClassOf(obo:MSIO_0000140 obo:OBI_0200169) + +# Class: obo:MSIO_0000141 (metabolite extraction) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000141 "ribose extraction"@en) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000141 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000141 "metabolite extraction is an extraction process which aims to retrieve small molecules known as metabolites, from a specimen"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000141 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000141 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000141 "metabolite extraction"@en) +SubClassOf(obo:MSIO_0000141 obo:OBI_0302884) + +# Class: obo:MSIO_0000142 (lipid extraction) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000142 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000142 "lipid extraction is an extraction which aims to retrieve lipid (hydrophobic carbohydrate) from a specimen"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000142 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000142 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000142 "lipid extraction"@en) +SubClassOf(obo:MSIO_0000142 obo:MSIO_0000141) + +# Class: obo:MSIO_0000143 (polar metabolite extraction) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000143 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000143 "polar metabolite extraction is a metabolite extraction which aims to retrieve water soluble or metabolites with polar solvent solubility properties. This is usually exclusive of hydrophobique, lipophile and lipid like metabolites."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000143 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000143 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000143 "polar metabolite extraction"@en) +SubClassOf(obo:MSIO_0000143 obo:MSIO_0000141) + +# Class: obo:MSIO_0000144 (cell layer enzymatic digestion) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000144 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000144 "cell layer enzymatic digestion is a material component separation process which uses an enzyme, usually a protease, to lyse the bonds between cultured cells and their substrates (usually a microplate, which may be coated with anchoring material such as collagen). Once the digestion is complete, cell layers can be harvested with minimal damage to the cells themselves."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000144 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000144 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000144 "cell layer enzymatic digestion") +SubClassOf(obo:MSIO_0000144 obo:OBI_0600014) + +# Class: obo:MSIO_0000145 (cell scraping) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000145 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000145 "cell scraping is a material component separation technique which uses mechanism means (as opposed to enzymatic ones) to detach cultured cells from the growth substrate. The technique is thought to be more aggressive and cause cellular breakage but has the benefit of avoiding use of enzymes, which may have their own side effects on cellular content."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000145 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000145 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000145 "cell scraping") +SubClassOf(obo:MSIO_0000145 obo:OBI_0600014) + +# Class: obo:MSIO_0000146 (centrifugation) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000146 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000146 "centrifugation is a material component separation process which relies on centrifugational forces applied by means of high velocity rotation to a sample placed in a vial or tube in a rotor, fixed to an centrifugation instrument."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000146 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000146 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000146 "centrifugation") +SubClassOf(obo:MSIO_0000146 obo:OBI_0600014) + +# Class: obo:MSIO_0000147 (gas chromatography) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000147 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000147 "gas chromatography is a material component separation process which use a mobile phase in gaseous form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in GC-MS applications."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000147 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000147 "GC"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000147 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000147 "gas chromatography"@en) +SubClassOf(obo:MSIO_0000147 obo:OBI_0600014) + +# Class: obo:MSIO_0000148 (high performance liquid chromatography) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000148 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000148 "high performance liquid chromatography is a kind of material component separation process which uses a mobile phase in liquid form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in LC-MS applications. the notion of high performance comes from the fact that higher pressure is applied to the liquid phase to pass material with adsorbant properties. Those may vary depending on the composition of the mobile phase (gradients between 2 solutions may be used)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000148 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000148 "HPLC"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000148 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000148 "adapted from https://en.wikipedia.org/wiki/High-performance_liquid_chromatography"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000148 "high performance liquid chromatography"@en) +SubClassOf(obo:MSIO_0000148 obo:OBI_0600014) + +# Class: obo:MSIO_0000149 (biomass) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000149 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000149 "biomass is a rate measurement datum of how much biochemical or biological material is produced over a period of time. it is usually reported in 'per hour'."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000149 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000149 "COSMOS"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000149 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000149 "biomass"@en) +SubClassOf(obo:MSIO_0000149 obo:OBI_0001554) + +# Class: obo:MSIO_0000150 (metabolic flux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000150 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000150 "Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway. Within cells, regulation of flux is vital for all metabolic pathways to regulate the metabolic pathway's activity under different conditions. Flux is therefore of great interest in metabolic network modelling, where it is analysed via flux balance analysis. + +amount per unit of time + +maybe normalized by protein content"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000150 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000150 "metabolic rate"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000150 "http://en.wikipedia.org/wiki/Flux_%28metabolism%29"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000150 "metabolic flux"@en) +SubClassOf(obo:MSIO_0000150 obo:OBI_0001554) + +# Class: obo:MSIO_0000151 (extracellular flux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000151 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000151 "An extracellular flux is a metabolic flux indicating the rate of absortion or release of a molecular entity by a cell system from or to its surroundings, respectively."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000151 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000151 " +https://www.microbialcellfactories.com/content/13/1/152"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000151 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000151 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000151 "extracellular flux"@en) +SubClassOf(obo:MSIO_0000151 obo:IAO_0000030) + +# Class: obo:MSIO_0000152 (metabolite excretion flux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000152 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000152 "an excretion flux is a metabolic flux indicating the rate of release of a metabolite by a cell system to its surroundings."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000152 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000152 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000152 "excretion rate"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000152 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000152 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000152 "metabolite excretion flux"@en) +SubClassOf(obo:MSIO_0000152 obo:MSIO_0000151) + +# Class: obo:MSIO_0000153 (metabolite uptake flux) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000153 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000153 "an uptake flux is a metabolic flux indicating the rate of absorption of a molecular entity by a cell system from its surroundings"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000153 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000153 "consumption rate"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000153 "uptake rate"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000153 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000153 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000153 "metabolite uptake flux"@en) +SubClassOf(obo:MSIO_0000153 obo:MSIO_0000151) + +# Class: obo:MSIO_0000154 (reaction rate) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000154 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000154 "the reaction rate is a rate measurement datum denoting a biochemical reaction as measured according to standard experimental methods."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000154 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000154 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000154 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000154 "reaction rate"@en) +SubClassOf(obo:MSIO_0000154 obo:OBI_0001554) + +# Class: obo:MSIO_0000155 (continuous fermentation cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000155 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000155 "continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added and product removed at a steady rate throughout the culture process. This is usually achieved using the specific type of fermenter known as a fed-batch culture reactor).") +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000155 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000155 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000155 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000155 "http://ib.bioninja.com.au/options/untitled/b1-microbiology-organisms/batch-versus-continuous.html") +AnnotationAssertion(rdfs:label obo:MSIO_0000155 "continuous fermentation cell culture"@en) +SubClassOf(obo:MSIO_0000155 obo:OBI_0100060) + +# Class: obo:MSIO_0000156 (double layer cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000156 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000156 "a cell culture population where cells are grown on top of each other, producing two layers of cells on the surface of the growth substrate, usually a flask or a petri dish"@en) +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000156 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000156 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000156 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000156 "double layer cell culture"@en) +SubClassOf(obo:MSIO_0000156 obo:OBI_0100060) + +# Class: obo:MSIO_0000157 (monolayer cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000157 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000157 "a cell culture population where no cells are grown on top of each other, producing a single layer of cells on the surface of the growth substrate, usually a flask or a petri dish"@en) +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000157 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000157 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000157 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000157 "monolayer cell culture"@en) +SubClassOf(obo:MSIO_0000157 obo:OBI_0100060) + +# Class: obo:MSIO_0000158 (sandwich cell culture) + +AnnotationAssertion(obo:IAO_0000112 obo:MSIO_0000158 "https://www.ncbi.nlm.nih.gov/pubmed/20109035") +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000158 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000158 "a sandwich cell culture is a type of cell culture population where the grown cells are in contact with a substratum at the bottom and the top, thereby providing a more defined boundary and level of interaction than in suspension grown cells or in classic monolayer cell cultures.") +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000158 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000158 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000158 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000158 "sandwich cell culture"@en) +SubClassOf(obo:MSIO_0000158 obo:OBI_0100060) + +# Class: obo:MSIO_0000159 (3D cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000159 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000159 "a 3D cell culture is a cultured cell population grown in conditions which better mimicks in-vivo growth environment (i.e. more effectively than a 2D culture) allowing more complex recapitulation of cellular processes. These cell cultures are achieved by used of scaffolding agents.") +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000159 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000159 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000159 "") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000159 "spheroid culture"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000159 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000159 "https://www.thermofisher.com/blog/cellculture/3d-culturing-leads-parkinsons-breakthrough/") +AnnotationAssertion(rdfs:label obo:MSIO_0000159 "3D cell culture"@en) +SubClassOf(obo:MSIO_0000159 obo:OBI_0100060) + +# Class: obo:MSIO_0000160 (chromatography column) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000160 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000160 "A Chromatography column is a device used in chromatography for the separation of chemical compounds. A chromatography column contains the stationary phase, allowing the mobile phase to pass through it. Chromatography columns of different types are used in both gas and liquid chromatography."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000160 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000160 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000160 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000160 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000160 "https://en.wikipedia.org/wiki/Chromatography_column"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000160 "chromatography column"@en) +SubClassOf(obo:MSIO_0000160 obo:OBI_0000968) + +# Class: obo:MSIO_0000161 (HPLC instrument) + +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000161 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000161 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000161 "An Instrument which is used to carry out a high performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography) technique. HPLC is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. + +The schematic of an HPLC instrument typically includes a degasser, sampler, pumps, and a detector. The sampler brings the sample mixture into the mobile phase stream which carries it into the column. The pumps deliver the desired flow and composition of the mobile phase through the column. The detector generates a signal proportional to the amount of sample component emerging from the column, hence allowing for quantitative analysis of the sample components. A digital microprocessor and user software control the HPLC instrument and provide data analysis."@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000161 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000161 "https://en.wikipedia.org/wiki/High-performance_liquid_chromatography"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000161 "HPLC instrument"@en) +SubClassOf(obo:MSIO_0000161 obo:OBI_0000968) + +# Class: obo:MSIO_0000162 (96-well microplate) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000162 "96-well microplate is an array of wells usually arranged in 8 rows of 12 columns whose volume range from 0.2 ml to 1.5 ml and which are used to grow cell or perform biochemical, in-vitro reactions. The material making up the plate may vary and may be surface treated in many custom way."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000162 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000162 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000162 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000162 "96-well microplate"@en) +SubClassOf(obo:MSIO_0000162 obo:OBI_0000967) + +# Class: obo:MSIO_0000163 (chemostat) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000163 "a chemostat is a device to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant. By changing the rate with which medium is added to the bioreactor the growth rate of the microorganism can be easily controlled. It allows culture to reach physiological steady state and chemostat is often used to gather steady state data about an organism in order to generate a mathematical model relating to its metabolic processes. +The name chemostat stems from \"Chemical environment is static\". + +The most striking advantages of chemostats are two-fold: microorganisms can be kept at a constant environmental conditions until the cultivated microorganisms reach steady state, defined by their specific growth rate (μ) being in balance with the dilution rate (D). Once the system is equilibrated, the steady state data can be used for quantification of physiological parameters and metabolic rates of organisms, which are eventually required for the parameterization of mathematical models."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000163 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000163 "10.4319/lom.2014.12.432 +http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000163 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000163 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000163 "http://en.wikipedia.org/wiki/Chemostat"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000163 "chemostat"@en) +SubClassOf(obo:MSIO_0000163 obo:OBI_0000967) + +# Class: obo:MSIO_0000164 (coated microplate) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000164 "a coated microplate is a kind of microplate whom surface has been treated in some, for instance by covalently attaching protein such as antibodies and cell matrix molecules to favor cell growth or induce speficic cellular behavior. +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000164 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000164 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000164 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000164 "coated microplate") +SubClassOf(obo:MSIO_0000164 obo:OBI_0000967) + +# Class: obo:MSIO_0000165 (constantly fed-batch culture reactor) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000165 "a constantly fed-btach culture reactor is a device in which the feed rate of a growth-limiting substrate is constant, i.e. the feed rate is invariant during the culture."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000165 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000165 "CFBC"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000165 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000165 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000165 "http://en.wikipedia.org/wiki/Fed-batch_culture#Constantly-fed-batch_culture"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000165 "http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000165 "constantly fed-batch culture reactor"@en) +SubClassOf(obo:MSIO_0000165 obo:OBI_0000967) + +# Class: obo:MSIO_0000166 (exponentially fed-batch culture reactor) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000166 "an exponentially fed-batch culture reactor is a device which deliver the ability to grow cells in a way non too dissimilar to that of a chemostat based culture, meaning that the cells are in a quasi steady-state condition."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000166 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000166 "EFBC"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000166 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000166 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000166 "http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000166 "exponentially fed-batch culture reactor"@en) +SubClassOf(obo:MSIO_0000166 obo:OBI_0000967) + +# Class: obo:MSIO_0000167 (fermenter) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000167 "A container in which fermentation takes place."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000167 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000167 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000167 "COSMOS tracer based metabolomics working group"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000167 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000167 "fermenter") +SubClassOf(obo:MSIO_0000167 obo:OBI_0000967) + +# Class: obo:MSIO_0000168 (flask) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000168 "a flask is a kind of container used for cell culture, and which is available in an array of material (usually transparent plastic polymer) which may be surface treated."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000168 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000168 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000168 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000168 "flask") +SubClassOf(obo:MSIO_0000168 obo:OBI_0000967) + +# Class: obo:MSIO_0000169 (petri dish) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000169 " a petri dish is a container used to grow cells or perform biochemical reactions, which used to be made of glass, but which is now available in a variety of surface treated or non-treated plastic polymers. a petri dish is a thin cylinder with the upper part acting as a lid, resting on small peg, large enough to enable gaseaous exchanges but still preventing water evaporation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000169 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000169 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000169 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000169 "petri dish") +SubClassOf(obo:MSIO_0000169 obo:OBI_0000967) + +# Class: obo:MSIO_0000170 (uncoated microplate) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000170 "a uncoated microplate is a kind of microplate whom surface has not received any treatment and is uniquely made of polymer."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000170 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000170 "EU H2020 PhenoMenAl") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000170 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000170 "uncoated microplate") +SubClassOf(obo:MSIO_0000170 obo:OBI_0000967) + +# Class: obo:MSIO_0000171 (mass spectrometry instrument) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000171 obo:IAO_0000423) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000171 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000171 "mass spectrometry instrument"@en) +SubClassOf(obo:MSIO_0000171 obo:OBI_0000932) + +# Class: obo:MSIO_0000172 (NMR instrument) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000172 obo:IAO_0000423) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000172 "import from NMRMLCV +"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000172 "NMR instrument"@en) +SubClassOf(obo:MSIO_0000172 obo:OBI_0000832) + +# Class: obo:MSIO_0000173 (high dose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000173 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000173 "high dose is a dose specifically set to trigger strong response in the system it is administered to, those effects may be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system).") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000173 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000173 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000173 "high dose"@en) +SubClassOf(obo:MSIO_0000173 obo:OBI_0000984) + +# Class: obo:MSIO_0000174 (low dose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000174 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000174 "low dose is a dose specifically set to trigger no or very limited response in the system it is administered to, those effects are not expected to be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000174 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000174 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000174 "low dose"@en) +SubClassOf(obo:MSIO_0000174 obo:OBI_0000984) + +# Class: obo:MSIO_0000175 (lethal dose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000175 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000175 "a \"lethal dose\" represents a dose (usually recorded as dose per kilogram of subject body weight) at which a given percentage of subjects will die."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000175 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000175 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000175 "https://en.wikipedia.org/wiki/Lethal_dose"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000175 "lethal dose"@en) +SubClassOf(obo:MSIO_0000175 obo:OBI_0000984) + +# Class: obo:MSIO_0000176 (lethal dose 50) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000176 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000176 "the \"lethal dose 50\" represents a dose (usually recorded as dose per kilogram of subject body weight) at which 50% of subjects will die."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000176 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000176 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000176 "LD50"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000176 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000176 "https://en.wikipedia.org/wiki/Lethal_dose"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000176 "lethal dose 50"@en) +SubClassOf(obo:MSIO_0000176 obo:MSIO_0000175) + +# Class: obo:MSIO_0000177 (medium dose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000177 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000177 "medium dose is a dose specifically set to trigger limited but clear response in the system it is administered to, those effects are not expected to be toxic but may be. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000177 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000177 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000177 "medium dose"@en) +SubClassOf(obo:MSIO_0000177 obo:OBI_0000984) + +# Class: obo:MSIO_0000178 (NOAEL dose) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000178 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000178 "noael dose is a dose defined as the highest experimental point that is without adverse effect."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000178 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000178 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000178 "No Observed Adverse Effect Level dose"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000178 "https://en.wikipedia.org/wiki/No-observed-adverse-effect_level"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000178 "NOAEL dose"@en) +SubClassOf(obo:MSIO_0000178 obo:OBI_0000984) + +# Class: obo:MSIO_0000181 (batch cell culture) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000181 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000181 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000181 "continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added at the begining of the culture process and products removed at the end.") +AnnotationAssertion(obo:IAO_0000116 obo:MSIO_0000181 "classes could be moved to become subclasses of 'cell culture process'") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000181 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000181 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000181 "EU H2020 PhenoMenAl") +AnnotationAssertion(rdfs:label obo:MSIO_0000181 "batch cell culture") +SubClassOf(obo:MSIO_0000181 obo:OBI_0100060) + +# Class: obo:MSIO_0000182 (fluxomics investigation) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000182 "fluxomics is a kind of investigation which aims at identifying, quantifying the fluxes of molecules in cellular systems and understanding the cellular metabolism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000182 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000182 "cosmos tracer based metabolomics working group"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000182 "fluxomics investigation"@en) +SubClassOf(obo:MSIO_0000182 obo:OBI_0000066) +SubClassOf(obo:MSIO_0000182 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectUnionOf(obo:MSIO_0000100 obo:MSIO_0000101))) + +# Class: obo:MSIO_0000184 (mass isotopomer fractional abundance) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000184 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000184 "mass isotopomer fractional abundance is a measurement data item corresponding to the following: the most abundant species is given the value 100 and all other species are normalized relative to 100 and expressed as percent relative abundance. + +fractional abundance of Mx=Ax= (abundance Mx) / ∑(i=0..n) abundance Mi, where Mx represents mass isotopomer Mx. + +"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000184 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000184 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000184 "mass isotopomer distribution"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000184 " + https://www.ncbi.nlm.nih.gov/pubmed/10362629 +"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000184 "mass isotopomer fractional abundance"@en) +SubClassOf(obo:MSIO_0000184 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000184 ObjectSomeValuesFrom(obo:BFO_0000050 obo:MSIO_0000077)) + +# Class: obo:MSIO_0000185 (steady state isotopic labeling experiment) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000185 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000185 "steady state labeling experiment is a material processing used in fluxomics studies where cells cultures are grown continuously in the presence of radiolabeled tracer compound throughout multiple platings. The redistribution of the label into metabolic intermediates and end-products is analysed when the system has reached an isotopic and metabolic steady state."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000185 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000185 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000185 "steady state isotopic labeling experiment"@en) +SubClassOf(obo:MSIO_0000185 obo:MSIO_0000096) +SubClassOf(obo:MSIO_0000185 ObjectSomeValuesFrom(obo:OBI_0000293 obo:MSIO_0000031)) + +# Class: obo:MSIO_0000186 (m over z) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000186 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000186 "the m/z notation is used for the independent variable in a mass spectrum. The mass-to-charge ratio (m/Q) is a physical quantity that is most widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger electron spectroscopy, cosmology and mass spectrometry.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000186 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000186 "adapted from wikipedia: +https://en.wikipedia.org/wiki/Mass-to-charge_ratio") +AnnotationAssertion(rdfs:label obo:MSIO_0000186 "m over z") +SubClassOf(obo:MSIO_0000186 obo:IAO_0000109) + +# Class: obo:MSIO_0000187 (corrected m/z) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000187 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000187 "a m over z ratio which underwent a correction data transformation to take into account variations caused by a specific aspects of the data acquisition process.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000187 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000187 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000187 "corrected m/z") +SubClassOf(obo:MSIO_0000187 obo:MSIO_0000186) + +# Class: obo:MSIO_0000188 (reference corrected m/z) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000188 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000188 "a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound and its spectral characteristics.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000188 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000188 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000188 "reference corrected m/z") +SubClassOf(obo:MSIO_0000188 obo:MSIO_0000187) + +# Class: obo:MSIO_0000189 (reference and adduct corrected m/z) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000189 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000189 "a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound, its spectral characteristics as well as the contributions caused by adducts generated during the ionization process.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000189 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000189 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000189 "reference and adduct corrected m/z") +SubClassOf(obo:MSIO_0000189 obo:MSIO_0000187) + +# Class: obo:MSIO_0000190 (retention time) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000190 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000190 "Retention time (RT) is a measure of the time taken for a solute to pass through a chromatography column. It is calculated as the time from injection to detection.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000190 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000190 "https://www.chromatographytoday.com/news/autosamplers/36/breaking-news/understanding-the-difference-between-retention-time-and-relative-retention-time/31166") +AnnotationAssertion(rdfs:label obo:MSIO_0000190 "retention time") +SubClassOf(obo:MSIO_0000190 obo:IAO_0000109) +SubClassOf(obo:MSIO_0000190 ObjectSomeValuesFrom(obo:IAO_0000039 ObjectUnionOf(obo:UO_0000010 obo:UO_0000031))) + +# Class: obo:MSIO_0000191 (peak area) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000191 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000191 "The area of a peak is a kind of data derived from a spectrum which is proportional to the product of its height and its width of a spectrum peak, but the proportionality constant depends on the peak shape.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000191 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000191 "adapted from: +https://terpconnect.umd.edu/~toh/spectrum/Integration.html") +AnnotationAssertion(rdfs:label obo:MSIO_0000191 "peak area") +SubClassOf(obo:MSIO_0000191 obo:MSIO_0000074) + +# Class: obo:MSIO_0000192 (normalized corrected peak area) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000192 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000192 "a normalized corrected peak area is a type of peak area which is produced followed a normalization data transformation and correction in order to make spectra comparable.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000192 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000192 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000192 "normalized corrected peak area") +SubClassOf(obo:MSIO_0000192 obo:MSIO_0000191) + +# Class: obo:MSIO_0000193 (total m/z signal intensity integrating over the whole peak with baseline substraction) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000193 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000193 "Signal intensity of all m/z values after integrating the whole peak and subtracting baseline"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000193 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000193 "peak area as signal intensity"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000193 "EU H2020 PhenoMenAl"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000193 "cosmos tracer based metabolomics working group") +AnnotationAssertion(rdfs:label obo:MSIO_0000193 "total m/z signal intensity integrating over the whole peak with baseline substraction"@en) +SubClassOf(obo:MSIO_0000193 obo:MSIO_0000074) + +# Class: obo:MSIO_0000194 (chemical entity assignment) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000194 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000194 "chemical entity assignment is an annotation which uses spectral information to assign and identify and molecular entity/chemical compound. Various methods manual and computer assisted may be used.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000194 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000194 "") +AnnotationAssertion(rdfs:label obo:MSIO_0000194 "chemical entity assignment") +SubClassOf(obo:MSIO_0000194 obo:IAO_0000030) + +# Class: obo:MSIO_0000195 (assignment by database search) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000195 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000195 "assignment by database search is a type of chemical entity assignment which relies on probing chemical electronic libraries and chemical databases to determine matching structure and thereby attempt to assign a chemical identity. Searches may rely on InChi string or keys for instance.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000195 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000195 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000195 "assignment by database search") +SubClassOf(obo:MSIO_0000195 obo:MSIO_0000194) + +# Class: obo:MSIO_0000196 (direct assignment to standard) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000196 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000196 "chemical entity assignment by direct assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to match the signature and affirm identity based on the spectral features found in the sample.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000196 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000196 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000196 "direct assignment to standard") +SubClassOf(obo:MSIO_0000196 obo:MSIO_0000194) + +# Class: obo:MSIO_0000197 (indirect assignment to standard) + +AnnotationAssertion(obo:IAO_0000114 obo:MSIO_0000197 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000197 "chemical entity assignment by indirect assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to infer chemical properties about another compound found in the sample.") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000197 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000197 "MSIO") +AnnotationAssertion(rdfs:label obo:MSIO_0000197 "indirect assignment to standard") +SubClassOf(obo:MSIO_0000197 obo:MSIO_0000194) + + +############################ +# Named Individuals +############################ + +# Individual: obo:MSIO_0000068 (Biocrates AG) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000068 "Biocrates Life Sciences AG, a biotechnology company, develops and markets targeted metabolic phenotyping solutions that support the discovery and validation of biomarkers for complex multifactorial diseases in pre-clinical and clinical research. The company offers mass-spectrometry based reproducible and quantitative kits and services that analyze various endogenous metabolites; and tools for insight into pathways and metabolic signatures of diseases, such as cancer or neurodegenerative diseases. It also offers metabolic phenotyping, and biomarker discovery and development services."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000068 "Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000068 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000068 "Biocrates Life Sciences AG"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000068 "https://www.bloomberg.com/research/stocks/private/snapshot.asp?privcapId=20741978"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000068 "Biocrates AG"@en) +ClassAssertion(obo:OBI_0000245 obo:MSIO_0000068) + +# Individual: obo:MSIO_0000093 (Agilent Technologies) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000093 "Agilent Technologies is an American public research, development and manufacturing company established in 1999 as a spin-off from Hewlett-Packard. The resulting IPO of Agilent stock was the largest in the history of Silicon Valley at the time. + +The company provides analytical instruments, software, services and consumables for the entire laboratory workflow."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000093 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000093 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000093 "Agilent"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000093 "https://en.wikipedia.org/wiki/Agilent_Technologies"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000093 "Agilent Technologies"@en) +ClassAssertion(obo:OBI_0000245 obo:MSIO_0000093) + +# Individual: obo:MSIO_0000097 (Bruker AG) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000097 "Bruker Corporation is a manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis. It is headquartered in Billerica, Massachusetts and is the publicly traded parent company of Bruker Scientific Instruments (Bruker AXS, Bruker BioSpin, Bruker Daltonics and Bruker Optics) and Bruker Energy & Supercon Technologies (BEST) divisions."@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000097 "Bruker"@en) +AnnotationAssertion(obo:IAO_0000118 obo:MSIO_0000097 "Bruker Corporation"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000097 "https://en.wikipedia.org/wiki/Bruker"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000097 "Bruker AG"@en) +ClassAssertion(obo:OBI_0000245 obo:MSIO_0000097) + +# Individual: obo:MSIO_0000098 (Thermo Fisher Scientific) + +AnnotationAssertion(obo:IAO_0000115 obo:MSIO_0000098 "Thermo Fisher Scientific is an American multinational biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific."@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000098 "Alejandra Gonzalez-Beltran"@en) +AnnotationAssertion(obo:IAO_0000117 obo:MSIO_0000098 "Philippe Rocca-Serra"@en) +AnnotationAssertion(obo:IAO_0000119 obo:MSIO_0000098 "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific"@en) +AnnotationAssertion(rdfs:label obo:MSIO_0000098 "Thermo Fisher Scientific"@en) +ClassAssertion(obo:OBI_0000245 obo:MSIO_0000098) + +) \ No newline at end of file diff --git a/src/ontology/msio-idranges.owl b/src/ontology/msio-idranges.owl new file mode 100644 index 0000000..48d3fdf --- /dev/null +++ b/src/ontology/msio-idranges.owl @@ -0,0 +1,53 @@ +## ID Ranges File +Prefix: rdf: +Prefix: idsfor: +Prefix: dce: +Prefix: xsd: +Prefix: allocatedto: +Prefix: xml: +Prefix: idprefix: +Prefix: iddigits: +Prefix: rdfs: +Prefix: idrange: +Prefix: owl: + +Ontology: + + +Annotations: + idsfor: "MSIO", + idprefix: "http://purl.obolibrary.org/obo/MSIO_", + iddigits: 7 + +AnnotationProperty: idprefix: + + +AnnotationProperty: iddigits: + + +AnnotationProperty: idsfor: + + +AnnotationProperty: allocatedto: + +Datatype: idrange:1 + + Annotations: + allocatedto: "ONTOLOGY-CREATOR" + + EquivalentTo: + xsd:integer[>= 0 , <= 999999] + + +Datatype: idrange:2 + + Annotations: + allocatedto: "ADDITIONAL EDITOR" + + EquivalentTo: + xsd:integer[>= 1000000 , <= 1999999] + + +Datatype: xsd:integer +Datatype: rdf:PlainLiteral + diff --git a/src/ontology/msio-odk.yaml b/src/ontology/msio-odk.yaml new file mode 100755 index 0000000..58cad98 --- /dev/null +++ b/src/ontology/msio-odk.yaml @@ -0,0 +1,65 @@ +id: msio +title: "Metabolomics Standards Initiative Ontology" +github_org: ISA-tools +git_main_branch: master +repo: MSIO + - base + - full +primary_release: full +export_formats: + - owl + - obo + - json +import_group: + use_base_merging: TRUE + products: + - id: iao + - id: cl + use_base: TRUE + - id: obi + use_base: TRUE + - id: chebi + mirror_from: https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/refs/heads/main/chebi_slim.owl + is_large: TRUE + - id: duo + make_base: TRUE + - id: ro + use_base: TRUE + - id: nmrCV + mirror_from: http://nmrml.org/cv/v1.1.0/nmrCV.owl + make_base: TRUE + base_iris: + - http://nmrML.org/nmrCV# + - id: chmo + use_base: TRUE +# - id: gaz +# make_base: TRUE +# base_iris: +# - http://purl.obolibrary.org/obo/gaz_ + - id: go + use_base: TRUE + - id: ms + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/MS_ + - id: ncbitaxon + mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl + - id: pato + use_base: TRUE + - id: uo + make_base: TRUE + - id: ogms + make_base: TRUE + - id: pr + make_base: TRUE + mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl + is_large: TRUE + - id: so + make_base: TRUE +robot_java_args: "-Xmx16G" +robot_report: + use_labels: TRUE + fail_on: ERROR + custom_profile: TRUE + report_on: + - edit \ No newline at end of file diff --git a/src/ontology/msio.Makefile b/src/ontology/msio.Makefile new file mode 100644 index 0000000..020996a --- /dev/null +++ b/src/ontology/msio.Makefile @@ -0,0 +1,26 @@ +## Customize Makefile settings for msio +## +## If you need to customize your Makefile, make +## changes here rather than in the main Makefile + +## Allowing inferred equivalent classes to allow UO + +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner $(REASONER) --equivalent-classes-allowed all --exclude-tautologies structural --annotate-inferred-axioms false \ + relax $(RELAX_OPTIONS) \ + reduce -r $(REASONER) $(REDUCE_OPTIONS) \ + remove --base-iri $(URIBASE)/PREFER --axioms external --preserve-structure false --trim false \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ +# Full: The full artefacts with imports merged, reasoned. +$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner $(REASONER) --equivalent-classes-allowed all --exclude-tautologies structural \ + relax $(RELAX_OPTIONS) \ + reduce -r $(REASONER) $(REDUCE_OPTIONS) \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ +# ---------------------------------------- \ No newline at end of file diff --git a/src/ontology/profile.txt b/src/ontology/profile.txt new file mode 100644 index 0000000..87246f4 --- /dev/null +++ b/src/ontology/profile.txt @@ -0,0 +1,32 @@ +WARN annotation_whitespace +ERROR deprecated_boolean_datatype +ERROR deprecated_class_reference +ERROR deprecated_property_reference +ERROR duplicate_definition +WARN duplicate_exact_synonym +WARN duplicate_label_synonym +ERROR duplicate_label +WARN duplicate_scoped_synonym +WARN equivalent_pair +WARN equivalent_class_axiom_no_genus +ERROR illegal_use_of_built_in_vocabulary +WARN invalid_xref +ERROR label_formatting +ERROR label_whitespace +INFO lowercase_definition +WARN missing_definition +WARN missing_label +WARN missing_obsolete_label +ERROR missing_ontology_description +WARN missing_ontology_license +ERROR missing_ontology_title +WARN missing_subset_declaration +INFO missing_superclass +WARN missing_synonymtype_declaration +ERROR misused_obsolete_label +ERROR misused_replaced_by +ERROR multiple_definitions +WARN multiple_equivalent_classes +ERROR multiple_equivalent_class_definitions +ERROR multiple_labels +WARN invalid_entity_uri \ No newline at end of file diff --git a/src/ontology/run.bat b/src/ontology/run.bat new file mode 100644 index 0000000..7f26e21 --- /dev/null +++ b/src/ontology/run.bat @@ -0,0 +1 @@ +docker run -v %cd%\..\..\:/work -w /work/src/ontology -e 'ROBOT_JAVA_ARGS=-Xmx16G' -e 'JAVA_OPTS=-Xmx16G' --rm -ti obolibrary/odkfull %* \ No newline at end of file diff --git a/src/ontology/run.sh b/src/ontology/run.sh new file mode 100755 index 0000000..99e7972 --- /dev/null +++ b/src/ontology/run.sh @@ -0,0 +1,164 @@ +#!/bin/sh +# Wrapper script for docker. +# +# This is used primarily for wrapping the GNU Make workflow. +# Instead of typing "make TARGET", type "./run.sh make TARGET". +# This will run the make workflow within a docker container. +# +# The assumption is that you are working in the src/ontology folder; +# we therefore map the whole repo (../..) to a docker volume. +# +# To use singularity instead of docker, please issue +# export USE_SINGULARITY= +# before running this script. +# +# See README-editors.md for more details. + +case "$@" in +*update_repo*) + # Execute a copy of this script so that it can be overwritten + # during the update process + mkdir -p tmp + sed -n '/^set -e/,$p' $0 > tmp/$0 + exec /bin/sh tmp/$0 "$@" + ;; +esac + +set -e + +# Check for spaces in the current directory path +for item in $PWD ; do + if [ "$item" != "$PWD" ]; then + echo "${0##*/}: error: repository path must not contain whitespace characters" >&2 + exit 1 + fi +done + +if [ -f run.sh.conf ]; then + . ./run.sh.conf +fi + +# Look for a GitHub token +if [ -n "$GH_TOKEN" ]; then + : +elif [ -f ../../.github/token.txt ]; then + GH_TOKEN=$(cat ../../.github/token.txt) +elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then + GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token) +elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then + GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") +fi + +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + +ODK_IMAGE=${ODK_IMAGE:-odkfull} +TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') +if [ -n "$TAG_IN_IMAGE" ]; then + # Override ODK_TAG env var if IMAGE already includes a tag + ODK_TAG=$TAG_IN_IMAGE + ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }') +fi +ODK_TAG=${ODK_TAG:-latest} + +ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx16G} + +ODK_DEBUG=${ODK_DEBUG:-no} + +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + +# Proxy settings for Java applications +[ -z "$HTTP_PROXY" ] && [ -n "$http_proxy" ] && HTTP_PROXY=$http_proxy +if [ -n "$HTTP_PROXY" ]; then + proxy_host=$(echo $HTTP_PROXY | sed -E 's,^https?://,,; s,:[0-9]+$,,') + proxy_port=$(echo $HTTP_PROXY | sed -E 's,^.*:([0-9]+)$,\1,') + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.proxyHost=$proxy_host" + [ "$proxy_port" != "$proxy_host" ] && ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.proxyPort=$proxy_port" +fi +[ -z "$HTTPS_PROXY" ] && [ -n "$https_proxy" ] && HTTPS_PROXY=$https_proxy +if [ -n "$HTTPS_PROXY" ]; then + proxy_host=$(echo $HTTPS_PROXY | sed -E 's,^https?://,,; s,:[0-9]+$,,') + proxy_port=$(echo $HTTPS_PROXY | sed -E 's,^.*:([0-9]+)$,\1,') + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttps.proxyHost=$proxy_host" + [ "$proxy_port" != "$proxy_host" ] && ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttps.proxyPort=$proxy_port" +fi +[ -z "$NO_PROXY" ] && [ -n "$no_proxy" ] && NO_PROXY=$no_proxy +if [ -n "$NO_PROXY" ] ; then + no_proxy_hosts=$(echo $NO_PROXY | tr ',' '|') + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.nonProxyHosts=$no_proxy_hosts" +fi + +TIMECMD= +if [ x$ODK_DEBUG = xyes ]; then + # If you wish to change the format string, take care of using + # non-breaking spaces (U+00A0) instead of normal spaces, to + # prevent the shell from tokenizing the format string. + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." + TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" +fi +rm -f tmp/debug.log + +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND +WORK_DIR=/work/src/ontology + +# Support for OAK cache sharing +if [ -n "$ODK_SHARE_OAK_CACHE" ]; then + case "$ODK_SHARE_OAK_CACHE" in + user) + # We assume the cache is in its default location; if it is not, + # ODK_SHARE_OAK_CACHE must point to the actual location. + ODK_SHARE_OAK_CACHE="$HOME/.data/oaklib" + ;; + repo) + ODK_SHARE_OAK_CACHE="$PWD/tmp/oaklib" + ;; + esac + [ $ODK_USER_ID -eq 0 ] && OAK_DEST=/root/.data/oaklib || OAK_DEST=/home/odkuser/.data/oaklib + VOLUME_BIND="$VOLUME_BIND,$ODK_SHARE_OAK_CACHE:$OAK_DEST" +fi + +if [ -n "$ODK_BINDS" ]; then + VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS" +fi + +if [ -n "$USE_SINGULARITY" ]; then + + singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ + --bind $VOLUME_BIND \ + -W $WORK_DIR \ + docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +else + BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /g')" + docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ + --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +fi + +case "$@" in +*update_repo*|*release*) + echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/." + ;; +esac \ No newline at end of file diff --git a/src/ontology/tmp/.gitkeep b/src/ontology/tmp/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100755 index 0000000..45d431d --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/sparql/README.md b/src/sparql/README.md new file mode 100644 index 0000000..be13c19 --- /dev/null +++ b/src/sparql/README.md @@ -0,0 +1,32 @@ +# Sparql checks + +[SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard +query language for RDF. This directory contains useful SPARQL queries +for perfoming over the ontology. + +SPARQL can be executed on a triplestore or directly on any OWL +file. The queries here are all executed on either msio-edit.obo or +downstream products in the [ontology](../ontology/) folder. We use +`robot` as this allows easy execution over any Obo-format or OWL file. + +We break the queries into 3 categories: + +## Constraint Violation checks + +These are all named `*violation.sparql`. A subset of these are +configured to be executed via travis. If these return any results, +then the build will fail. + +Consult the individual sparql files to see the intent of the check + +## Construct queries + +These are named `construct*.sparql`, and always have the form `CONSTRUCT ...`. + +These are used to generate new OWL axioms that can be inserted back +into the ontology. + +## Reports + +The remaining SPARQL queries are for informative purposes. A subset +may be executed with each release. \ No newline at end of file diff --git a/src/sparql/basic-report.sparql b/src/sparql/basic-report.sparql new file mode 100644 index 0000000..cff9773 --- /dev/null +++ b/src/sparql/basic-report.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 0000000..a6a4851 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix \ No newline at end of file diff --git a/src/sparql/dc-properties-violation.sparql b/src/sparql/dc-properties-violation.sparql new file mode 100644 index 0000000..981709d --- /dev/null +++ b/src/sparql/dc-properties-violation.sparql @@ -0,0 +1,11 @@ +# The purpose of this violation is to make sure people update +# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/) +# to using the recommended DC Terms namespace (http://purl.org/dc/terms/) +# See also discussion on https://github.com/oborel/obo-relations/pull/692 + +SELECT ?term ?predicate WHERE { + ?term ?predicate ?value . + FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} + diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql new file mode 100644 index 0000000..edf658b --- /dev/null +++ b/src/sparql/edges.sparql @@ -0,0 +1,18 @@ +prefix owl: +prefix rdfs: +prefix rdf: + +SELECT ?x ?p ?y +WHERE { + {?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty ?p ; + owl:someValuesFrom ?y ] + } + UNION { + ?x rdfs:subClassOf ?y . + BIND(rdfs:subClassOf AS ?p) + } + ?x a owl:Class . + ?y a owl:Class . +} diff --git a/src/sparql/illegal-date-violation.sparql b/src/sparql/illegal-date-violation.sparql new file mode 100644 index 0000000..6fcaeba --- /dev/null +++ b/src/sparql/illegal-date-violation.sparql @@ -0,0 +1,11 @@ +PREFIX dct: +PREFIX xsd: +PREFIX oboInOwl: + +SELECT DISTINCT ?term ?property ?value WHERE +{ + VALUES ?property {dct:date dct:issued dct:created oboInOwl:creation_date} + ?term ?property ?value . + FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$')) + FILTER (datatype(?value) != xsd:dateTime || !regex(str(?value), '^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z')) +} diff --git a/src/sparql/iri-range-advanced-violation.sparql b/src/sparql/iri-range-advanced-violation.sparql new file mode 100644 index 0000000..9df8a4f --- /dev/null +++ b/src/sparql/iri-range-advanced-violation.sparql @@ -0,0 +1,20 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX rdfs: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + rdfs:seeAlso + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) + FILTER (!isIRI(?value)) +} diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql new file mode 100644 index 0000000..b6f1a9c --- /dev/null +++ b/src/sparql/iri-range-violation.sparql @@ -0,0 +1,18 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) + FILTER (!isIRI(?value)) +} diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql new file mode 100644 index 0000000..c9c468c --- /dev/null +++ b/src/sparql/label-with-iri-violation.sparql @@ -0,0 +1,8 @@ +PREFIX rdfs: + +SELECT ?term ?value +WHERE { + ?term rdfs:label ?value . + FILTER (REGEX(?value, "http[s]?[:]")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} diff --git a/src/sparql/msio_terms.sparql b/src/sparql/msio_terms.sparql new file mode 100644 index 0000000..38f5f66 --- /dev/null +++ b/src/sparql/msio_terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql new file mode 100644 index 0000000..68ee7df --- /dev/null +++ b/src/sparql/multiple-replaced_by-violation.sparql @@ -0,0 +1,11 @@ +PREFIX replaced_by: + +SELECT DISTINCT ?entity ?property ?value WHERE { + VALUES ?property { + replaced_by: + } + ?entity ?property ?value1 . + ?entity ?property ?value2 . + FILTER(?value1!=?value2) + BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value) +} diff --git a/src/sparql/obsoletes.sparql b/src/sparql/obsoletes.sparql new file mode 100644 index 0000000..7aff433 --- /dev/null +++ b/src/sparql/obsoletes.sparql @@ -0,0 +1,14 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?replCls ?consCls WHERE { + ?cls a owl:Class ; + owl:deprecated "true"^^xsd:boolean . + OPTIONAL {?cls replaced_by: ?replCls} + OPTIONAL {?cls consider: ?consCls} +} +ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql new file mode 100644 index 0000000..79ca8e6 --- /dev/null +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -0,0 +1,11 @@ +PREFIX rdf: +PREFIX oio: +PREFIX owl: +PREFIX rdfs: + +SELECT ?term WHERE { + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } + UNION + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} diff --git a/src/sparql/postprocess-module.ru b/src/sparql/postprocess-module.ru new file mode 100644 index 0000000..0767af1 --- /dev/null +++ b/src/sparql/postprocess-module.ru @@ -0,0 +1,16 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +DELETE { + ?ontology ?ontology_annotation_property ?ontology_annotation_value . +} + +WHERE { + ?ontology rdf:type owl:Ontology . + ?ontology ?ontology_annotation_property ?ontology_annotation_value . + FILTER(?ontology_annotation_property != dc:source && ?ontology_annotation_property != rdf:type) + +} \ No newline at end of file diff --git a/src/sparql/preprocess-module.ru b/src/sparql/preprocess-module.ru new file mode 100644 index 0000000..99120a0 --- /dev/null +++ b/src/sparql/preprocess-module.ru @@ -0,0 +1,22 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +#DELETE { +# ?ontology ?ontology_annotation_property ?ontology_annotation_value . +#} + +INSERT { + ?ontology dc:source ?version_iri . +} + +WHERE { + ?ontology rdf:type owl:Ontology ; + owl:versionIRI ?version_iri . + #OPTIONAL { + # ?ontology ?ontology_annotation_property ?ontology_annotation_value . + #} + +} \ No newline at end of file diff --git a/src/sparql/redundant-subClassOf-violation.sparql b/src/sparql/redundant-subClassOf-violation.sparql new file mode 100644 index 0000000..3c64962 --- /dev/null +++ b/src/sparql/redundant-subClassOf-violation.sparql @@ -0,0 +1,14 @@ +PREFIX oio: +PREFIX owl: +PREFIX rdfs: + +SELECT ?term ?xl ?y ?yl ?z ?zl WHERE { + ?term rdfs:subClassOf ?y ; + rdfs:label ?xl . + ?y rdfs:subClassOf+ ?z ; + rdfs:label ?yl . + ?term rdfs:subClassOf ?z . + ?z rdfs:label ?zl . + + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql new file mode 100644 index 0000000..247fbde --- /dev/null +++ b/src/sparql/simple-seed.sparql @@ -0,0 +1,13 @@ +prefix owl: + +SELECT DISTINCT ?cls WHERE +{ + {?cls a owl:AnnotationProperty .} + UNION + {?cls a owl:ObjectProperty .} + UNION + {?x ?cls} + UNION + {?x ?cls} + FILTER (!isBlank(?cls)) +} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql new file mode 100644 index 0000000..5ca7e31 --- /dev/null +++ b/src/sparql/subsets-labeled.sparql @@ -0,0 +1,13 @@ +prefix oio: +prefix owl: +prefix inSubset: +prefix rdfs: + +SELECT ?subset ?clsLabel +WHERE +{ + ?cls a owl:Class ; + inSubset: ?subset ; + rdfs:label ?clsLabel +} +ORDER BY ?subset ?cls diff --git a/src/sparql/synonyms.sparql b/src/sparql/synonyms.sparql new file mode 100644 index 0000000..ba6b03a --- /dev/null +++ b/src/sparql/synonyms.sparql @@ -0,0 +1,26 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +SELECT ?cls ?pred ?val ?synType +WHERE + { ?cls ?pred ?val ; + a owl:Class . + FILTER ( + ?pred = rdfs:label || + ?pred = oboInOwl:hasRelatedSynonym || + ?pred = oboInOwl:hasNarrowSynonym || + ?pred = oboInOwl:hasBroadSynonym || + ?pred = oboInOwl:hasExactSynonym + ) + + OPTIONAL { + [ + a owl:Axiom ; + owl:annotatedSource ?cls ; + owl:annotatedProperty ?pred ; + owl:annotatedTarget ?val ; + oboInOwl:hasSynonymType ?synType + ] + } + } diff --git a/src/sparql/taxon-range-violation.sparql b/src/sparql/taxon-range-violation.sparql new file mode 100644 index 0000000..ba49820 --- /dev/null +++ b/src/sparql/taxon-range-violation.sparql @@ -0,0 +1,10 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: + +SELECT ?term ?property ?taxon +WHERE { + VALUES ?property { never_in_taxon: present_in_taxon: } + ?term ?property ?taxon . + FILTER (!isIRI(?taxon) || !STRSTARTS(STR(?taxon), "http://purl.obolibrary.org/obo/NCBITaxon_")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MSIO_"))) +} diff --git a/src/sparql/term-tracker-uri-violation.sparql b/src/sparql/term-tracker-uri-violation.sparql new file mode 100644 index 0000000..c91ba5f --- /dev/null +++ b/src/sparql/term-tracker-uri-violation.sparql @@ -0,0 +1,8 @@ +PREFIX xsd: +PREFIX term_tracker_item: + +SELECT ?term ?term_tracker ?term_tracker_type WHERE { + ?term term_tracker_item: ?term_tracker . + FILTER(DATATYPE(?term_tracker) != xsd:anyURI) + BIND(DATATYPE(?term_tracker) as ?term_tracker_type) +} diff --git a/src/sparql/terms.sparql b/src/sparql/terms.sparql new file mode 100644 index 0000000..ec58b4c --- /dev/null +++ b/src/sparql/terms.sparql @@ -0,0 +1,15 @@ +PREFIX rdf: +prefix owl: +SELECT DISTINCT ?term +WHERE { + { + ?s1 ?p1 ?term . + FILTER(?p1!=rdf:type) + } + UNION + { + ?term ?p2 ?o2 . + FILTER(?o2!=owl:Ontology) + } + FILTER(isIRI(?term)) +} \ No newline at end of file diff --git a/src/sparql/xrefs.sparql b/src/sparql/xrefs.sparql new file mode 100644 index 0000000..bde8fc9 --- /dev/null +++ b/src/sparql/xrefs.sparql @@ -0,0 +1,8 @@ +prefix oio: +prefix owl: + +SELECT ?cls ?xref WHERE +{ + ?cls a owl:Class ; + oio:hasDbXref ?xref +} diff --git a/workflows/docs.yml b/workflows/docs.yml new file mode 100644 index 0000000..b197a88 --- /dev/null +++ b/workflows/docs.yml @@ -0,0 +1,27 @@ +# Basic ODK workflow +name: Docs + +# Controls when the action will run. +on: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + push: + branches: + - master + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + build: + name: Deploy docs + runs-on: ubuntu-latest + steps: + - name: Checkout main + uses: actions/checkout@v4 + + - name: Deploy docs + uses: mhausenblas/mkdocs-deploy-gh-pages@master + # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + CONFIG_FILE: mkdocs.yaml + diff --git a/workflows/qc.yml b/workflows/qc.yml new file mode 100644 index 0000000..f3aae72 --- /dev/null +++ b/workflows/qc.yml @@ -0,0 +1,33 @@ +# Basic ODK workflow + +name: CI + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "ontology_qc" + ontology_qc: + # The type of runner that the job will run on + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.6 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v4 + + - name: Run ontology QC checks + env: + DEFAULT_BRANCH: master + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false +